Warning: spoilers for Mass Effect 1, 2 & 3 and Knights of the Old Republic.
At the last possible minute, the game took a nosedive in quality unmatched since the final episode of Battlestar Galactica, and replacing that controversial episode in the "WTF just happened?" canon of bad endings. The reaction of the fanbase can be best described as one of total bewilderment and, in some quarters, outright rage. The problem is not that the ending is bleak (no matter which choices you make at the end of the game, quiet a lot of people ending up dying), it's that it makes little to no sense with regard to plot logic and is massively inconsistent with the themes and storylines developed up until that point.
Backing up a little, this is obviously a blog mostly focused on books and many readers won't have a clue what's going on with this controversy. So first, some scene-setting. Obviously, MAJOR SPOILERS follow for the Mass Effect trilogy. I would advise against reading on if you plan to play these games at any point in the future.
The Citadel: 44km long, home to 15 million people and absolutely no public toilets visible anywhere.
Synopsis of the Mass Effect Trilogy
The Mass Effect games are set roughly 175 years into the future. Mankind has discovered a device at the edge of the Solar system (disguised as Pluto's moon, Charon*) that permits instantaneous travel to distant star clusters. Through this mass relay, it has made contact with a number of alien races who have joined together to form the Council, an interspecies UN which mediates conflicts and regulates interstellar trade and diplomacy**. The Council is based at the Citadel, a massive cylindrical space station*** of ancient, alien origin. As the trilogy opens Earth is campaigning hard for a senior seat on the Council, which is controversial due to the short period of time that Earth has been a player in galactic affairs. The player's character, Commander Shepard (who can be male or female, and of whatever ethnicity, sexuality or appearance the player chooses), is in line to become the first human Spectre, an agent with wide-ranging powers to deal with threats to the Council races in whatever manner he or she chooses.
In the original Mass Effect, Shepard is pitted against Saren, a turian Spectre who has gone rogue and allied himself with the geth, a race of robots (or synthetics, in the game's parlance). 300 years ago, the geth drove their creators, the quarians, into exile on a fleet of spacecraft**** and took over their mutual homeworld, Rannoch. Initially it appears that Saren and the geth are simply out for power and territory but Shepard, aided by allies from several races, uncovers evidence that Saren is being controlled by the ancient, alien spacecraft he is using as his flagship. The spacecraft, Sovereign, contacts Shepard at a critical juncture in the storyline and tells him (or her) that it is a sentient intelligence, a member of a race of entities known as the Reapers. Every 50,000 years the Reapers sweep through the Milky War, annihilating sophisticated, space-faring civilisations, throwing everything into chaos***** and leaving other races untouched. Sovereign refuses to divulge its motivations, stating that it is beyond the lesser races' comprehension. Eventually, Shepard discovers that the Citadel itself acts as an intergalactic mass relay, allowing the Reapers (who have spent almost 50,000 years in hibernation in 'darkspace', or intergalactic space) to invade and throw all the lesser races into total confusion. In a massive, climactic battle, Shepard kills Saren and destroys Sovereign at the Citadel, defeating the threat of an imminent Reaper invasion. During the game it is also revealed that the Reapers like to use a process called 'Indoctrination' to bring allies and minions under their full control. They see strange things that aren't there, have odd dreams, hear whispers and voices and ultimately start behaving very out-of-character to other people, but logically to themselves. This process takes months, possibly years, to fully complete.
Is he evil because he smokes or does he smoke because he's evil?
In Mass Effect 2, we discover that Shepard's warnings about the Reapers (who are now active and proceeding back to the Milky Way using 'standard' FTL drives, which are much slower) have fallen on deaf ears. An alien race known as the Collectors (servants of the Reapers) have begun raiding worlds in the Terminus Systems and in one battle, Shepard's ship, the Normandy, is destroyed and Shepard presumed killed. In reality he is rescued by Cerberus, an outlawed but formidably rich organisation which puts humans and the affairs of Earth ahead of the other races. Cerberus's boss, President Bartlet (er, the Illusive Man, voiced by Martin Sheen), reveals to Shepard that the Reapers are the greatest threat humanity has ever seen, and Shepard needs to be able to oppose them with unlimited resources, something he can't get through official channels. Shepard is given a new ship (also dubbed the Normandy) and collects together a band of a dozen experts in different areas of combat, research and investigation. They take the fight to the Collectors and their home base in the Galactic Core, eventually eliminating the threat (the player can choose to capture the Collector base or destroy it, which has ramifications going into Mass Effect 3). However, Cerberus's brutal and amoral nature is exposed in the process and Shepard and his crew quit in disgust. In a final twist (revealed in an extra downloadable mission, Arrival) it is revealed that the Reapers are approaching a mass relay on the Galactic Rim, which they can use to invade in force. Shepard destroys the relay with an asteroid, but the resulting blast destroys a batarian colony inhabited by over 300,000 colonists. Despite this, the Reaper invasion is delayed by several months. During these engagements Shepard also learns that the geth are actually a non-hostile species whom were under Reaper control during the events of the first game and drove the quarians off their homeworld only after the quarians tried to slaughter their creations in a genocidal fury.
Reapers can be unruly tourists.
At the start of Mass Effect 3, Shepard is being held on Earth for trial over his alleged war crimes and the wiping out of the batarian colony. The trial is cut short when the Reapers finally arrive in overwhelming force, destroying Earth's defences in a matter of minutes and occupying the planet. Shepard is rescued by the Normandy and his former commanding officer, Admiral Anderson, remains behind to organise a resistance. Shepard has to rally the races of the Galaxy to defeat the Reapers through sheer force of numbers, but the Reaper invasion is multi-pronged, targeting not just Earth but the homeworlds of several of the other major races: Palaven, the turian homeworld, is particularly badly hit. Shepard provides aid to Palaven by travelling to Tuchanka, the home planet of the fiercesome krogans, and curing them of a genetically-engineered disease designed to reduce their numbers. The krogan then enter the war, giving the turians enough of a breathing space to commit their fleet to an assault on Earth. Shepard also has to stop a war between the quarians and the geth. As revealed in the previous game, the geth are not actually a hostile species but had acted in self-defense. The quarians, who only want their homeworld back, are initially unsympathetic. When a Reaper attacks Rannoch, Shepard convinces both sides to join forces to destroy it. Afterwards, the two forces can agree to help Shepard and make peace (alternately, Shepard can side with one race against the other and wipe it out). Unfortunately, the last major race, the asari, lose their homeworld, Thessia, to a brutal and overwhelming Reaper attack that leaves the planet burning in space.
Throughout the last game, the humans and other races are building a device called the Crucible, which they believe is a Death Star-style superweapon that can wipe the Reapers out altogether. Unfortunately, the ancient designs for the weapon (which originated with a race called the Protheans, wiped out by the Reapers in the last 'cycle' 50,000 years ago) require the addition of a component called 'the Catalyst', which is of unknown origin and location. Shepard has to destroy the Cerberus organisation to uncover the location of the Catalyst: it's on, or part of, the Citadel, and the Illusive Man has already fled there. The Reapers, aware of this, capture the Citadel and move it into Earth orbit, deploying the bulk of their fleet to defend it.
Throughout the third game Shepard is under immense stress and starts to suffer bouts of depression and doubt. He has a recurring dream in which he sees a young boy (whom he saw killed on Earth at the start of the game) and tries to help him, only to see him consumed by flames. During this recurring dream Shepard hears voices of dead allies and other deceased characters speaking to him.
ALERT: Incoming deus ex machina.
The Controversial Ending
In the grand finale of the game and the trilogy, Shepard's allies muster an enormous fleet consisting of thousands of ships from around a dozen races and launch an overwhelming assault on Earth. Shepard, linking up with Anderson's rebels, leads a ground attack on the Reaper base in London, where a transportation beam has been established linking the Citadel to the ground. In a final assault on the beam location Shepard is extremely badly wounded, but is able to teleport to the Citadel, which the Reapers have turned into a charnel house of corpses.
The Reapers wiping out the citizens of the Citadel is a dark and bleak decision. The Citadel is a principal, major location in all three games. You spend tens of hours there, dealing with different crises and missions and interacting with hundreds of characters. The game turning around and slaughtering all of them (and the 15 million people who reportedly live on the station) is gutsy, risking making the player feel like everything they did on the Citadel in the series was in vain. But it dramatically ramps up the stakes. A planet like Thessia getting blown away is hardcore, as it has a major emotional impact on the asari characters in the game (including a major party and storyline character, Liara), but you never visit there before a brief mission in Mass Effect 3 so it doesn't have much resonance for the player personally. Devastating the Citadel and killing every single character of note you've met who lives there is a much more serious gut-punch. Whilst a lot of people dislike this storyline choice, ultimately I applaud BioWare for being prepared to do something that seriously annoys people whilst having a rational and understandable role in the endgame of the story.
The rest of the ending, however, leans towards the nonsensical. Shortly after arriving on the Citadel, Shepard is contacted by Anderson, who has also managed to teleport aboard. Shepard makes his way to a control room in a hidden part of the Citadel (though where exactly it is hidden is unclear, since it seems to be on the central command-and-control tower of the Citadel, an area of extremely limited space which people have been living in for thousands of years) and is confronted by both Anderson and the Illusive Man. The Illusive Man claims that the Citadel and the Crucible can be used together to take control of the Reapers and propel humanity forwards thousands of years in technology and science, making them the dominant race in the Galaxy. Anderson rejects this, saying the Reapers must be destroyed utterly to prevent this 50,000-year cycle of annihilation from continuing. Both Anderson and Shepard tell the Illusive Man that he has been Indoctrinated by the Reapers. In an inexplicable moment, the Illusive Man seems to take control of both Shepard and Anderson and has Shepard shoot Anderson (but, bizarrely, a copy of the bullet wound appears on Shepard). Depending on your dialogue choices in this exchange, the Illusive Man can kill Anderson outright, but be talked into committing suicide by Shepard, or can kill both Anderson and Shepard (obviously causing a game over sequence and forcing a reload). However, Shepard can also shoot the Illusive Man first. This done, he opens up the Citadel, allowing the Crucible to dock. Anderson has a final moment of peace before dying. Shepard, still suffering from the weird gunshot wound, passes out whilst trying to figure out how to make the Crucible work.
At this point the tattered, wounded and bleating remnants of logic finally slink away and out of sight. The area of floor Shepard is lying on suddenly levitates and flies through the ceiling onto the top of the Citadel, where the Crucible's tip has docked. At this point a glowing blue entity appears, taking the form of a young human child (the same one in Shepard's dreams)****** and has a bit of a chat with Shepard, who has now weirdly stopped bleeding. The entity claims that it is the Catalyst. It created the Reapers millions of years ago (possibly a billion years ago based on the age of one of the derelict Reapers in Mass Effect 2) as its solution to a problem. Every few thousand years, sentient organic life develops within the Milky Way and ultimately develops a synthetic servitor race, which is either mistreated and rebels or ultimately concludes that the organic creator races are obsolete and utterly destroys them. To avoid this problem, the Reapers retard the development of organic lifeforms. They 'harvest' selected races to make new Reapers and insure that their technological and biological distinctiveness are integrated into their own make-up*******, then wipe out the rest of the races and allow the primitive species to go unmolested so they can grow up and ascend to the stars themselves (and be destroyed by the Reapers next time around).
Yeah, run that one past us again?
However, the Catalyst has worked out after several tens of thousands of repetitions of the cycle that it's rather unsatisfying as a solution (impressive, as most players had spotted enormous logic failures in it before the glowing blue space kid had even finished monologuing). With the Crucible brought to its front door and with an organic representative of the various races on hand (i.e. Shepard), the Catalyst is willing to try a different approach. It offers Shepard three choices: he can Destroy the Reapers, as Anderson wanted, annihilating them forever. This will end the current war, but without the Reapers on hand another synthetic race will arise in the future and annihilate all organic species. This will also destroy all other synthetic species, including the geth. Or Shepard can choose to Control the Reapers, as the Illusive Man wanted. The Reapers will leave (with it left unclear whether the cycle will continue in another 50,000 years or if the Reapers will depart forever). The final option - and the one presented as the best possible ending - is Synthesis: Shepard can merge synthetic and organic DNA, effectively transforming all lifeforms in the Galaxy into cyborgs. Newly-emerging synthetic and organic life will be absorbed into this new paradigm, ending the threat of future wars and mass slaughter.
When shooting an explosive control panel do you 1) shoot it from a distance and live, or 2) walk towards it whilst shooting, ensuring you are caught in the resulting explosion?
In all three endings, however, the mass relays will be destroyed, since they will be needed to transmit the Crucible's signal across the Galaxy and will be demolished in the process. Also, Shepard will die in all three choices: Control will see his physical form deleted and his essence absorbed into the Catalyst so he can order the Reapers around; Synthesis absorbs his already-fused essence (Shepard is technically a cyborg due to the implants used by Cerberus to resurrect him in Mass Effect 2) and uses it as the template for the merging of the two forms of life; and Destroy, er, causes a big explosion that Shepard will walk into because it looks kind of awesome in the cut-scene. I'm a bit hazy on why he has to die in that solution. The solutions also have different impacts on the Citadel: in Control the Citadel survives okay (leaving at least the possibility that there may be survivors in remote parts of the station) but in the other two the station is wracked by massive explosions that seem to incinerate the Crucible and the central core of the station and shear off two of its arms, though, contrary to some fan complaints, the station isn't shown being unambiguously destroyed and plummeting to Earth (which would probably wipe out whoever's left standing down there, given that the Citadel's massive size would result in an explosion that would dwarf the meteor impact that caused the extinction of the dinosaurs).
No matter what ending you choose, the Crucible's energy is shown spreading through the mass relay network, spreading across the entire Galaxy and collapsing relay after relay. And the Normandy is shown diving through a mass relay, trying to outrun the energy wave, but is eventually hit by it and forced to crash on a jungle planet. Several survivors are shown stumbling out of the wreckage (if you chose Synthesis, they are show glowing with slightly weird green energy).
If you chose Destroy and got an insanely high 'military preperation' score earlier in the game, you also get a curious brief cut-scene in which a figure that seems to be Shepard (the face is obscured), lying amidst some debris (which looks nothing like the Citadel), suddenly taking a deep breath.
You then get a post-credits sequence in which an old man is telling his grandson stories about 'The Shepard' and how he saved the Galaxy (arguably in all three endings you do neutralise the Reaper threat successfully). When the kid asks for another story, the old man agrees.
Something the ending gets right: a badass space battle.
The endings are unsatisfying on numerous levels. The most notable is in terms of dramatic structure. This argument has been superbly made by Jim Stevenson on his blog, The Writer's Block. Briefly, he argues that the ending of the game fails because it introduces a major, game-changing element (the starchild/glowing space kid) extremely late in the day and completely out of the blue. It also disrupts the traditional structure of the Hero's Journey, in which the denouncement (in which Shepard gets to talk to his friends and companions before launching the battle in London) takes place before the actual ending on the Citadel, an ending which lacks either clarity or catharsis.
On top of that complaint, the ending fails on a thematic level. Whether synthetic and organic life can coexist is a major subplot of the latter two games in the series; whilst the quarian/geth struggle was given a lot of screen-time in both Mass Effect 2 and 3, it was not a major thematic question, at least not compared to the themes of cooperation and coexistence. In an additional twist, the Normandy's artificial intelligence, EDI, is given a robotic body in Mass Effect 3 and spends the game considering the nature of her existence before deciding to ally wholeheartedly with the organics and develop a romantic relationship with a human character. Both of these plots basically say that it is possible for synthetic and organic life to live together and coexist without an outside force making that decision for them. The game's ending goes against this. Even more bizarrely, Shepard is not able to raise this logical objection to the Catalyst during their conversation.
Buzz Aldrin provides the voice of the old geezer in the post-credits sequence, restoring a tiny amount of geek-cred to proceedings.
It is also not possible for Shepard to ask the Catalyst what the hell is up with the whole Reaper plan anyway, since creating a race of synthetics to destroy organics every 50,000 years so they won't make synthetics that will destroy them seems somewhat unnecessary (since they die anyway, with the difference being that the Reapers allow some primitive races to survive) and convoluted. Shepard also fails to ask the Catalyst why it was necessary to do the whole thing with Sovereign and Saren in Mass Effect 1, since the Catalyst could have presumably activated the Citadel's mass relay and brought the Reaper fleet into the Galaxy years before the invasion, completely catching everyone off-guard and slaughtering them with no chance of a counter-attack like the one Shepard has led. It's possible that the Catalyst was inert or inactive before the arrival of the Crucible, but it's still unclear why Sovereign wouldn't have been able to activate it during the original game. It's also left unclear why the Catalyst is okay with Shepard making the choice. If the Catalyst was unhappy with the 'Reaper Cycle' plan (because it's more than slightly bonkers) and knew that it could use the Crucible and an organic/synthetic hybrid like Shepard to enact a different, better plan which didn't cause so much mayhem and death, why not just let the Crucible be built and brought to it, and invite Shepard up to discuss the situation over tea and biscuits?
Another massive problem with the ending, and one of its single weakest elements (and one I think hasn't been that much reported), is that Shepard is allowed to make the choice because he is a hybrid, thanks to his Cerberus implants that brought him back from the dead. The problem with this is that both Mass Effect 2 and 3 spend some considerable time and effort making it clear that Shepard is still human, and his implants are not that special. Whilst he has some synthetic parts to him, calling him a hybrid or a cyborg is a bit of a stretch and an exaggeration. Ironically, this problem could have been fixed. We see the Illusive Man controlling Shepard briefly in the finale, so dialogue could have been inserted making it clear that Cerberus's meddling and reconstruction was far more serious and notable than it first appeared, allowing the Illusive Man to control him and also qualifying him as more 50-50 human/synthetic, making the Catalyst's choice of him make a lot more sense. Instead, based on the info we have, Shepard is insufficiently hybridised to be able to make the choices he does, and in particular to make the Synthesis ending make any sense (notably, Shepard doesn't have that weird green glowing thing going on that your team-mates on the Normandy are shown exhibiting a few moments later).
"Let's get the hell out of here!"
"I don't know!"
Another considerable problem, and one that seems to be 100% universally loathed, even by people who otherwise like the ending, is what is going on with the Normandy at the end of the game. Before the assault on London, the Normandy is shown engaging the Reaper forces over Earth in a huge space battle. Shepard and his entire crew land on Earth, including characters not on your immediate squad (you can only have two team-mates with you) and a whole bunch of characters from the first two games who are leading assaults on different fronts, and join the battle. During the final push for the transportation beam, Shepard is almost hit by a Reaper laser and knocked out. When you wake up seconds later (the Reaper who hit you is shown powering down its laser and taking off), your squad-mates have vanished (unless you have a really low military readiness score, in which case you see them lying dead on the ground near you) and you press on. Maybe 10-15 minutes pass between this point and the end of the game. When the end of the game kicks in, the Normandy is shown trying to escape the Solar system through the Charon mass relay, is caught in a blast on the far side and forced to crash-land on some jungle planet. From the ship, several crewmembers emerge. Whilst the choice of crewmembers is somewhat randomised and somewhat dependent on earlier game choices, it's normal to see one or both of your squad-mates from the London mission emerge from the wreckage of the Normandy, even if you had a low score and saw them dead in London.
This bit of the ending makes zero sense whichever way you cut it. The planet is - probably due to the near-identical terrain and an almost identical skyscape showing two large moons - 2175 Aeia, a planet visited in Mass Effect 2 (in Jacob Taylor's loyalty mission). To get there from Earth requires multiple relay jumps (not just one) and the planet is in a different star system to the nearest relay, requiring a standard, time-consuming FTL jump. The Normandy simply wouldn't have been able to get there in time (it actually wouldn't have had enough time to have travelled from Earth to the Charon relay, let alone anywhere else) before the relays blew.
More to the point, there is no reason for them to have tried to flee the system. Even if your team-mates on Earth thought you were incinerated and retreated (which is at least implied by radio chatter you hear whilst waking up, suggesting all ground forces are pulling out and you are assumed dead), it seems unlikely they would simply turn and flee on the Normandy, especially since the rest of the space fleet was holding its own against the Reapers (as seen later on, the space forces are able to deliver the Crucible to the Citadel without Reaper interference due to the strength of their forces). It's also odd no attempt was made by the Normandy to contact Shepard during the end-game. You receive a radio transmission from Admiral Hackett, commanding the human forces in the space fleet, so there's no radio jamming going on, and you and Anderson talk freely on the radio whilst in different parts of the Citadel. Of course, if the Normandy crew could contact you, then it could swing by and rescue you with incredible ease (the whole Catalyst conversation takes place on the docking ring of the Citadel, literally a few hundred metres away from where the Normandy used to dock in all three games). The ending section with the Normandy makes so little sense that fans have used it as final, conclusive proof that the entire end of the game is a hallucination taking place completely within Shepard's fevered brain.
Saren, Indoctrinated and proud (note: not romanceable in-game).
Say What? Or Welcome to the Indoctrination Theory
The "It was all a dream!" ending is rightly regarded as a monstrous cop-out whenever it is deployed in story-telling. It's a rather damning comment on the ending to Mass Effect 3 that fans are rather desperately hoping it is just a dream, and the real, 'true' ending to the story will be revealed in future DLC (Downloadable Content) that retcons the end of the game. However, there is a surprisingly large amount of in-game evidence that suggests this theory could actually be true.
As mentioned in the summaries, the Reapers have been shown to have the ability to take over lesser lifeforms. Most of the times this is quick and violent, resulting in the creation of murderous 'husks' (basically space zombies) with no intelligence. Over the course of many years, however, the Reapers can fully Indoctrinate people into becoming their minions without them even realising this is happening. They did this twice in Mass Effect, to Saren and an asari matriarch, and in Mass Effect 3 have successfully done this to the Illusive Man. In the latter case, they have convinced the Illusive Man that he is working for the betterment of humanity and against the Reapers. If you force the Illusive Man to realise the truth (by letting him kill Anderson and then aggressively arguing with him), he is so horrified he commits suicide on the spot.
This leads to the ultimate question: what if Shepard has been Indoctrinated? This would be major narrative coup if BioWare could pull it off, as tricking the character means tricking the player whilst also laying down adequate foreshadowing so it's not just totally random.
This foreshadowing exists. In order to become Indoctrinated, it is necessary for the subject to spend time inside Reapers, or to come into contact with Reaper technology. In Mass Effect 1 Shepard speaks to a Reaper at some length and undertakes a spacewalk along the side of the Citadel in close proximity to Sovereign. In Mass Effect 2 Shepard spends a significant amount of time inside a derelict Reaper (the exact same Reaper that drove an exploration party mad through a form of Indoctrination) and confronts a major artifact of Reaper technology in the endgame. In Arrival Shepard spends several days in contact with a Reaper artifact that has already Indoctrinated several people around it. Also, Shepard's reconstruction at the start of Mass Effect 2 may only have been possible with Reaper technology (the same technology that is shown later permitting the Indoctrination of the Illusive Man). In short, there are multiple moments in the preceding two games where it is possible she (or he) was Indoctrinated, to the point where it seems implausible he (or she) hasn't been Indoctrinated before Mass Effect 3 even begins.
Is he really there? Hopefully not, because then at least it reduces the amount of cheese in the intro.
The next thing to do is identify symptoms of Indoctrination in Shepard's behaviour. One of the first signs is seeing things that aren't there. Early in the game, as Shepard and Anderson try to escape from the Reaper's initial assault, Shepard finds a young boy hiding in a ventilation shaft. The boy, weirdly, refuses Shepard's help and abruptly vanishes when Anderson returns to talk to Shepard (who, also rather oddly, doesn't mention him to Anderson). Later, Shepard sees the same boy coming out of a building and boarding one of the evacuation shuttles, only for the shuttle to be shot down by a Reaper. Careful viewing of this sequence shows that no-one on the shuttle notices the boy or tries to help him up, and that when the shuttle explodes and Shepard winces, none of his crew-mates standing next to him are shown reacting. Shepard then spends the rest of the game experiencing nightmares in which he runs around a forest at night trying to save the boy, only to see him consumed by fire. As the dreams recur, ghostly whispers can be heard around Shepard which resolve into the voices of characters who have died over the course of the three games**** ****. Towards the end of the game, during the final race to the transport beam, Shepard even sees the same trees from his dream dotting the landscape. This definitely qualifies as the 'hearing voices' and 'seeing things that aren't there' symptoms associated with Indoctrination. There's also a lot of talking about Indoctrination in the game, from the fully-voiced Codex entry that goes into it in some detail to a pair of asari discussing it in the background in the Citadel medical centre. There's even an odd moment on the Normandy when one of your squadmates starts talking about a hum which you cannot hear (Indoctrination can be backed up by ultrasonic noises according to the Codex).
Once Shepard has been hit by the beam, passes out, and wakes up, the theory is he is now in the grip of a hallucination, during which his subconscious is battling the effects of Indoctrination. This explains why getting to the beam and onto the Citadel seems a rather surreal, dreamlike experience, taking place partly in slow motion with Shepard wielding a gun with infinite ammo, and how Shepard finds a part of the Citadel that no-one's seen before, despite it being located on one of the most prominent, regularly-visited parts of the station. The theory goes that Anderson and the Illusive Man are figments of your imagination, sitting on your shoulders like a guardian angel and a devil-like figure of temptation. Listen to Anderson and you can survive this section. Listen to the Illusive Man and you die. Once you're past that part, you then have to make your final choice: give into the Catalyst (in the theory the Catalyst is actually Harbinger, the Reaper who was the main enemy of Mass Effect 2 and is the Reaper that shoots you at the start of this section) and accept Indoctrination (by accepting Control or Synthesis) or reject Indoctrination by choosing Destroy. Provided your score is high enough, you wake up back in the rubble of the London street, ready to rejoin the fight (having had a nice hallucinatory vision of your friends on the Normandy surviving a crash-landing in the meantime).
Shepard lives! Maybe.
It's a nice idea, and certainly solves the problems with the ending. Provided you survive, it means that nothing after you get hit by the beam is real. That means the Citadel may not be as badly damaged as it first appeared, it means the Illusive Man is still around and the battle for Earth and the Galaxy is not yet decided. Essentially, it means we can get a less problematic ending which makes sense (even if it's still a dark or bleak one).
However, is it likely? Would BioWare really want to execute a plot twist of this magnitude? And the answer to that is emphatically yes.
In 2003, BioWare released Star Wars: Knights of the Old Republic. This was a very fine computer RPG and one of the very best Star Wars games ever made. One of its most notable features was a stunning late-game twist in which it was revealed that your character was in fact the main villain of the setting at the time. It turned out that the Jedi had captured the dastardly Darth Revan, blanked his memory to try and turn him back to the Light Side, lost contact with him and had him basically turn into the player character. Since Revan, like most Sith Lords, covered his face in public, no-one had a clue your character was him (including you, due to the amnesia). It was a spectacular twist, foreshadowed superbly and deftly executed. In the history of the Star Wars universe, only the "I am your father," moment from Empire Strikes Back can compete with it.
So certainly BioWare are more than capable of pulling off a twist like this (it's also worth noting that there's an excellent plot twist, if not quite of the same magnitude, in BioWare's Jade Empire as well), which of course leads to the obvious question: why didn't they?
"Yo Reapers, I got your Indoctrination Theory right here!"
The Indoctrination Theory is so well-supported by in-game evidence that many fans are confidently expecting BioWare to reveal it is true. However, there are issues with it. The biggest is...why not have it in the game?
As mentioned at the Writer's Block above, if the game had ended with Shepard waking up in London and then carrying on the fight with the Indoctrination Theory explained, it would have been awesome. It would have challenged the Knights of the Old Republic plot twist for effectiveness and impact. It would have been ballsy and cool. Yet they didn't. Why?
The cynical answer is that they plan to give us the ending as paid DLC. However, that doesn't seem right. It's one thing to give out optional bonus stuff as DLC (like the Mass Effect 2 add-ons Arrival and Lair of the Shadow Broker) or optional characters (like Javik in Mass Effect 3 itself), but withholding the actual game's ending from the public? That would be bizarre. It's true that Fallout 3 had a problematic ending which Bethesda quickly fixed with Broken Steel a few months later, but that was a far smaller problem, easily fixed in about sixty seconds after you've installed the expansion. Rewriting Mass Effect 3's ending would require substantial amounts of new content and gameplay after your rejoin the action, including lots of voice-overs from major actors (to keep costs down, previous Mass Effect DLC has previously relied solely on one or two voice actors appearing). It's a huge amount more work, likely unprecedented for a piece of DLC. Even more of an issue, having denied gamers the 'real' ending, if BioWare tried charging for the 'real' ending, it would make the controversy that's developed so far seem feeble in comparison.
Unfortunately, it appears that the more prosaic explanation for the theory is correct: it's an idea that was developed during the game's production, but then downplayed when the ending was finally created in favour of a mystery (or, as the game's producer put it, "Lots of speculation from everyone!"), possibly also due to time running out as the ending was programmed in November, not long before they had to lock the game so it could get its necessary Sony and Microsoft certifications before the game could be released.
If this is the case, it is unlikely that the ending will be changed significantly. Maybe a more clarified ending which explains why the Normandy was fleeing the system, but beyond that I'd be surprised to see things changed too much. Which is a shame because the Indoctrination Theory really does explain a lot of things that are otherwise just bizarre.
As it stands, Mass Effect 3's ending dents a seriously enjoyable series of computer role-playing games and, on a larger scale, is yet another weird, vague and oddball ending to a long-running SF story. Coming on the heels of the endings to Lost and Battlestar Galactica, it does make one yearn for a story that actually ends with a fully logical and explicable conclusion. But that's a totally different topic to discuss at another time.
* This is reminiscent of Roger Macbride Allen's SF novel The Ring of Charon, which also sees human scientists discover an FTL device hidden within Charon.
** A bit like Star Trek's United Federation of Planets.
*** A cross between the titular space station of Babylon 5 and Arthur C. Clarke's Rama.
**** Yes, very much like Battlestar Galactica.
***** Yes, a bit like the Shadows in Babylon 5.
****** Yes, a bit like the Starchild in 2001: A Space Odyssey and its sequels.
******* Yes, a bit like the Borg.
**** **** Yes, like the whispers in the jungle on Lost.
It's worth checking out original Mass Effect writer Drew Karpyshyn's ending as they envisaged it whilst working on the first two games in the series. This ending was ditched long before Mass Effect 3 went into production, but it does at least explain why the synthetic/organic conflict is not such a key focus in the earlier games.