The Entire Internet has decided that the ending to MASS EFFECT 3 is terrible, torpedoing not just the otherwise excellent conclusion to the series but also rendering the entire trilogy a waste of time.

Whilst I would not go that far, the ending - if taken at face value - is indeed made up of horrible writing and incoherent ideas. It is thematically and tonally inconsistent with the rest of the trilogy before it and riddled with nonsensical plot holes that make no sense whatsoever. It manages to invoke not just one but two entries from The Massive Book of Terrible Cliches That Should Never, Ever Be Used Again, which is great going. We get the 'hitherto unknown true enemy showing up to explain WTF is going on through a weird conversation' sequence (see: Neo vs the Architect in MATRIX RELOADED) followed by the 'post credits, centuries years later this is the impact your decisions had' cliche (see: BSG finale).

Of course, there is a reason the ending is ill-conceived. The original ending would have revealed that the Reapers are destroying sentient life to spare it from the horrific oblivion which will be unleashed by the spread of Dark Energy through the universe. This ending was ditched after it leaked in a design document last year, so BioWare decided to change it.

Now the Reapers are destroying organic life (after harvesting the best examples of it from each 50,000-year-long cycle) because if they don't, they will develop their own synthetic servitors who will inevitably destroy them.

Yeah.

Now, obviously that's nonsensical (if the Reapers kill organic life or their own future-cylons do it, so what, they're going to die anyway, why not let them have a few tens of thousands of years of fun in the meantime?). It also doesn't help that as a theme it doesn't have a huge amount to do with the rest of the games: the geth and EDI storylines are not dominant prior to MASS EFFECT 3 itself (when they suddenly become so, as clumsy foreshadowing for the ending). In addition, two of the key themes of the series are that the different races can learn to coexist peacefully, as you prove when you peacefully unite the quarians and geth in ME3 itself, and the power of the freedom of choice. In the finale it is not possible to continue this process. You either have to wipe out all synthetic life (including the now-peaceful geth and EDI, your own allied AI character), forcibly turn everyone into cyborgs (denying them the right of free choice) or take control of the Reapers and exile them from the galaxy forever (which sounds okay until you realise it will destroy the FTL Mass Relays, as indeed the other two choices do).

In short, the three different endings are not that different: you die anyway and the Mass Relays are destroyed and FTL travel is shut down regardless. The only difference is that in the Destroy ending, EDI and the geth are all slaughtered as well, whilst in Control they are not. In both cases we are told the cycle will resume millennia down the line and the organic races will be wiped out. Synthesis is presented as the best option by the Reapers - it ends the cycle by creating a new paradigm where synthetics and organics coexist as the same form of life - but it also turns Shepard into a kind of monstrous god, converting everyone in the galaxy against their will into cyborgs. In addition, it should be treated with suspicion as Synthesis is what the Reapers were doing (on their more brutal terms, merging a few million lifeforms with synthetic technology and killing everyone else).

Where the biggest problem kicks in is that with Destroy, you are told that it's your own cybernetic implants (in place after your revival at the start of ME2) will kill you. But they don't. Presuming you got a high enough military effectiveness score, you actually live. A later credits sequence shows Shepard surviving. Which is weird as it proves that the Reapers are lying their heads off about what is going on (some players have also reported seeing EDI getting out of the Normandy having chosen Destroy, which also indicates the Reapers are lying, but it's possible that's a bug with the wrong animated sequence triggering).

The ending is thus nonsensical from the point of view of internal logic. We also need to add the bit of the ending where the Normandy - at that point in orbit around Earth - is suddenly showing fleeing to another system through a Mass Relay before it blows. Erm, why? Where are they going? How did they get to the relay when moments before they were at Earth? How did your team-mates from the final mission in London get back to the Normandy in the few minutes the end of the game covers? Why were they cutting and running when it looked like you were winning?

Fans have come up with a possible solution, but it's rather cynical if BioWare are doing this. The game is seeded with frequent suggestions that Shepard may have been indoctrinated by the Reapers. There are repeated, numerous references to indoctrinated people seeing things that are not there, having weird visions and dreams and hearing voices. The final sequence of the game, from when Shepard is hit by Harbinger's beam in London, is surreal and weird. Shepard has a weapon with infinite ammo which appears in this sequence. Paragon and Renegade choices are reversed (if Shepard does not choose the Renegade actions twice in a row in the final confrontation, first Anderson and then himself will die, despite the actions not being Renegade in the slightest). Black specks around the edge of the screen similar to those in his dream sequences appear. The trees from Shepard's dreams are present around the transport beam at the end of the game. The Reaper intelligence takes the form of the boy Shepard has been dreaming about all game for no particular reason (a boy, btw, that no-one else sees or interacts with at the start of the game when he's supposedly there in the flesh). It's also worth noting that the Reaper intelligence is shown gloating if you choose Control or Synthesis, but vanishes almost instantly if choose Destroy. And we know it's lying about Destroy if Shepard can survive it (and only it). Finally, if Shepard chooses Destroy and lives, he wakes up in the rubble and wreckage of what appears to be London, not on the Citadel (unless the Citadel mysteriously turns out to have been built with concrete).

The conclusion, therefore, is that Shepard's final confrontation in the game is actually a hallucination brought about by an attempt at Reaper Indoctrination. Choosing Control or Synthesis permits the Reapers' victory and sees Shepard fall under the Reapers' control. Choosing Destroy frees Shepard from the Reapers' control. If you have a high enough score, Shepard can survive the process and presumably resume the fight in a future expansion or DLC.

There's certainly more than enough evidence to support the Indoctrination Theory (the thread discussing it at BioWare's website was well north of 400 pages long on the last count and BioWare personnel have been directing complainants to read that thread). We know from interviews and storyboards released by BioWare on an iPhone app that indoctrination was going to play a bigger role in the game (with Shepard falling prey to it in the final moments of the game and losing control of his limbs, though still being able to talk) but they took it out, or at least de-emphasised it. So certainly it's an idea that was in their minds when writing the ending.

The problem, going forwards, is that this means we will get additional DLC or stuff to resolve the ending. If it's free, that's okay but feels weird if you've just paid £30 (or $60 or whatever) for the game and then have to wait several months to get the 'real' ending. If it isn't free, then it would feel like a desperate money-grab by EA and BioWare which would likely wreck whatever goodwill the gaming community has left for them.

The sad alternative is that BioWare left this stuff in to make players think about it, but have no plans to make the ending clearer and have left the game with these illogical and bizarre choices which don't make much sense. In either case, it was really not a good idea.

Still, the other 99% of the game was excellent