Bear in mind that this post includes MASSIVE SPOILERS about Mass Effect 3, and its ending in particular. Also, it should go without saying that some of what I discuss is particular to my particular playthrough of the series (female Shepard, about 90-95% Paragon, relationship with Liara through all 3 games, kept as many people alive as possible, etc.). Your mileage may vary (and that's the beauty of it). So, without further ado, my thoughts on ME3:
Overall, I thought ME3 was excellent. I think it really works as a concluding chapter for the series and brings many personal and galactic storylines to a satisfying, if sometimes bittersweet, end. One way or another, you decide the future of the Krogan and the genophage, and the outcome of the Quarian-Geth war (and play out the deeply personal investment that Wrex, Mordin, Tali, and Legion have in those stories). You also see Samara reunited with the last of her daughters, Miranda finally confront her father, etc. There were also some beautifully quiet and tender non-sex moments between my Shepard and her lover, Liara.
I thought the opportunity to delve into the secrets of the past of the galaxy was quite cool. Seeing how the Protheans shaped the younger races, especially the Asari (as revealed on Thessia), was fascinating. I also thought that Javik was an extremely interesting character, especially considering how uncompromising and brutal-minded he was, and how that contrasted with the mythology of the Protheans that many characters like Liara, and the whole Hanar culture, had become attached to. I do think it's worth noting that Javik was a soldier who lived his entire life in the very last days of his species' losing war with the Reapers, so he's not necessarily a typical Prothean in that respect.
Speaking of the Protheans, the fact that the crucible was not originally a Prothean design, but was secretly passed down from one dead civilization to the next across many cycles of extinction turns the epic factor up to 11 and gives even more weight to the story. Cool.
The general theme of ME3's main quest is uniting the races of the galaxy in the face of desperation and terror for one last stand, together. That's pretty epic and awesome as sci-fi/fantasy plots go, if a little overused. The execution is great, though, and, in my Paragon-heavy storyline, that often involves making peace between old enemies so that they can both have a future. So many videogames are about war, but rarely have I felt a more meaningful sense of accomplishment in a game than making peace between the Krogan and Turians, or the Quarians and the Geth. It also makes Mordin and Legion's self-sacrifice especially meaningful.
Now for the infamous ending. First, I recommend you have a look at Gabe's thoughts on the matter and the backlash from some fans, which I largely agree with (agree with Gabe, that is).
Here is my interpretation of the final part of the game: activating the crucible allows Shepard to meet the God-like AI that controls the citadel and the reapers. Shepard is wired up with cybernetics and is the recent victim of a nearly-successful indoctrination attempt by the Illusive Man, so I think that it absolutely makes sense that the citadel-AI is able to read images from her mind and take the form of what her subconscious has been obsessing about (as evidenced by her dreams). Just as the reapers are able to indoctrinate organics and lesser synthetics (i.e. the heretic Geth), the citadel-AI indoctrinates the reapers to carry out its plan. I think this helps explain the reapers' motivations and their utter implacability quite well (illustrated by the almost frantic insistence of the reaper on Rannoch that the cycle MUST continue).
As for the citadel-AI's actual plan: it is to harvest the most advanced organic civilizations every 50K years so that they don't develop to the point that they create a race of synthetics that is so advanced it is able to completely eradicate all other sentients. The Geth, who were created a scant 300 years before the reaping, could easily develop into this (although, fortunately, the Geth are self-preserving and not actually genocidal, but they do think BIG, as evidenced by their attempt to build a gigantic Dyson sphere to house their complete collective consciousness). Even without rogue AIs, advanced organic races can easily become oppressive. Javik reveals that the Prothean empire was hardly a utopia, and they were fairly iron-fisted in their treatment of other races in their cycle. So, the basic idea is to prune the "tallest trees" of organic civilization in each cycle so that others can grow and flourish in their own time. Obviously wiping out civilizations sucks, but it makes a certain sort of sense. Each cycle has 50K years of civilization, of art, science, and culture. All of that is beautiful and meaningful even if it eventually ends, and from the perspective of the citadel-AI, it is necessary for a handful of generations out of every couple thousand to face their annihilation for all of that to continue.
Now for the nature of the reapers themselves. Note that the citadel-AI says that civilizations are "archived" in reaper form. The way I interpret that is that the thoughts and personalities of the organics that are harvested to construct reapers are integrated and subsumed in the new reaper's consciousness. Because of the overriding imperative to continue the cycle that the citadel-AI's indoctrination forces on the reapers, we never really see much of that. It is hinted at, however, when Legion talks about the vast, awesome, unknowable thoughts of reaper minds. I interpret those thoughts as being the collective zeitgeist of whole civilizations that were harvested to create those reapers. In a way, those civilizations live on as reaper minds. Harvesting suddenly makes a LOT more sense, as just using organic bodies as raw material in reaper construction is stupid and unnecessary (even if it were for some reason chemically necessary, it would be a lot less hassle for the reapers to just get the materials from algae or cyanobacteria), so I give this explanation a lot of credit for resolving my biggest problem with Mass Effect 2's ending.
Moving on to Shepard's choices in the ending: It's true that, in all of the possible endings, Shepard sacrifices herself in some way. In the "red" (destroy the reapers) ending, she basically wrecks the citadel, although there is a hint that she survived in the rubble if you go in with a very high readiness rating. In the "blue" (control the reapers) ending, she merges herself with the citadel, essentially becoming a new AI controller for the reapers. In the "green" ending, she sacrifices herself in order to "imprint" herself on all organics AND synthetics in the galaxy and create a future where both forms of intelligence are integrated and synergistic. It's true that no matter what ending you choose, Shepard sacrifices herself to change the future. I'm fine with that. Heroic self-sacrifice is a big theme in ME3 (Mordin and Legion, again, come to mind), and Shepard giving her life in the end is a lot more meaningful than the alternative.
Now for my interpretation of the differences between the endings. If you choose to destroy the reapers, you're basically saying fuck the citadel, fuck the reapers (and fuck EDI and the innocent Geth, sadly), fuck the cycle: the chaos of naturally developing life is preferable to an imposed order that requires periodic genocide. Now, it is possible that the citadel-AI was right all along and that this will result in the eventual extinction of organic life. It is also possible that the memory of the reapers will serve as a powerful warning to future civilizations and that there will be a tremendous cultural aversion to AIs, eventually reaching the status of a mythological/religious commandment and forcing the development of organic potential instead. This is almost exactly the backstory of the Dune universe, where AIs are viewed as horrible, sinful abominations, and genetically engineered, pharmaceutically enhanced, and exceptionally trained humans perform the tasks which would otherwise require advanced computers.
If you choose to control the reapers, Shepard does what the Illusive Man thought he was trying to do, which is to turn the tables on the reapers and use their immense power in the service of organics. On the one hand, this will fast-forward the technological sophistication of galactic civilization like crazy. On the other hand, this basically makes Shepard-AI the God of the Milky Way. Shepard-AI will probably be a benevolent God, but this future is one of ultimate order, with Shepard-AI and her vast fleet of reapers in near-absolute control of the direction of galactic civilization.
Finally, there is the ending which I chose, the "synergy" between organic and synthetic life. I admit this was the least-explained and hardest to understand of the endings, but I also think it is potentially the most hopeful and bright. Instead of annihilating the synthetics or assuming the mantle of godhood, Shepard ends indoctrination and "changes" all organics and synthetics in the galaxy to incorporate eachother. The process for this may seem magical and handwavy, but I think it's plausible in the ME universe because: 1. Reapers are able to use nanobots to create husks from organic corpses in a matter of seconds. 2. Sovereign's reaper indoctrination worked across a distance of many lightyears. 3. The citadel-AI, as creator and controller of the reapers, is presumably even more technologically advanced than they are (perhaps being to the reapers as the reapers are to us). As Arthur C. Clarke said, "any sufficiently advanced technology is indistinguishable from magic". I believe the citadel-AI is certainly sufficiently advanced, and technology required to pull off the galactic transformation is consistent with what's already been seen in the ME series.
With the "how" of the synergy ending addressed, I'll talk about about what I think happened and what the outcome is. I think all organics become partly cybernetic, and all synthetics get their programming modified. My interpretation of "synergy" is that, through the cybernetics and the new programming, all sentients, whether organic or synthetic (reapers included) are now connected to each other in some way, via some sort of universal empathy for each other or low-level telepathy and sharing of thoughts. The Zhu's Hope colony on Feros, after the Thorian was destroyed, is a good example of this. The colonists are all still individuals, but they can on some level feel each others' emotions and act as one for each others' benefit. I interpret the synergy ending as magnifying this to a galactic scale, where organics and synthetics are individuals, but deeply and integrally linked to each other. This may be my hippie utopian fantasy, but the idea of universal, natural peace and love between all beings really appeals to me. Note, also, that the reapers are now free from indoctrination and part of this union. Now, instead of unknowable objects of terror and dread, the reapers are grand and beautiful creatures that carry the thoughts and memories of dead civilizations into the future.
Obviously I had to do some thinking and extrapolation of my chosen ending on my own, but having done so I think it is wonderful. I didn't need everything spelled out exactly for me, and thinking through the implications on my own proved to be a very edifying experience. The final image of Joker and EDI arm-in-arm, as Gabe notes, powerfully illustrates this future.
To wrap things up, I'll address a few of the complaints people had about the ending.
- "Destroying the mass relays would wipe out all of the systems where they are stationed." It's true that it's established in the "arrival" DLC for ME2 that destroying a mass relay releases a tremendous amount of energy that basically wipes out anything in the same host star system. Put another way, each mass relay stores a vast amount of potential energy which is released when it is destroyed. Now consider the process by which the mass relays are destroyed at the end of ME3: they are destroyed while propagating a signal which destroys or controls the reapers, or transforms all life in the galaxy. Also consider the fact that reapers (and organic life) are present in many systems which do not have a mass relay. It isn't unreasonable to assume that the power of that signal as it radiates from each mass relay follows an inverse-square law, and must cover an extremely large volume with sufficient power. My interpretation is that all of that potential energy in the mass relays, instead of being destructively discharged all willy-nilly as in "Arrival", is actually used to boost the signal so that it covers the entire galaxy. That also explains why it was necessary to destroy the mass relays in the first place: their energy sources are needed.
- "Without the mass relays, galactic civilization is boned." It's not quite as bad as all that. It's true you won't be able to get from one end of the galaxy to the other in a matter of days anymore, but there are still conventional FTL drives in starships that at least allow for short-range interstellar travel to be possible. Also, background in ME3 establishes that quantum entanglement communicators, which allow instantaneous point-to-point communication and don't in any way depend on the mass effect, have seen a big uptake. Without a way of delivering a replacement terminal, the existing QECs should be protected very carefully, but the network of QECs effectively makes communication (with telepresence, VR, and all that good stuff) possible on a galactic scale, even if physical travel is limited to local star clusters. Also remember that the Prothean scientists on Ilos were able to build their own mass relay to the citadel, so it's entirely reasonable that with concerted scientific effort on the part of the galaxy's still-communicating civilizations, the technology to build mass relays could be redeveloped. In the "green" and "blue" endings, reaper tech is still available to accelerate this process (even without mass relays, reaper FTL drives are implied to be VERY fast, since the reapers still managed to get back from dark space in a couple of years despite Shepard preventing them from using mass relays).
- "The allies that Shepard brought to the battle of Earth are now marooned and screwed." It's true that many of the allies Shepard brought to Earth will probably never return home. Keep in mind, though, that they all signed up for a suicide mission, so surviving at all is a win in itself. Also keep in mind that, as I noted above, they may not be able to physically travel home in their lifetimes, but they can still communicate with their loved ones across the galaxy. There are a couple of sub-issues with this that I address below.
- "Turian and Quarian biochemistry is based on dextro-amino-acids, so they can't eat Earth food and will starve." The point about Earth food is true, the point about starvation isn't. Remember that the Quarian fleet refitted their liveships (basically massive space farms) with dreadnought-class cannons for the battle of Rannoch. After the Quarian civilians were settled on Rannoch, the flotilla joined the battle at Earth, and you can explicitly see Quarian liveships (the massive ships with spherical main hulls) among the allied fleet. A few of these liveships provided food for 17 million Quarians. If just one of them survived the battle for earth, it could easily provide food for the surviving Quarian and Turian military forces at Earth (and its stocks of crops could be used to seed other food-production facilities for them).
- "Without Wrex's leadership, and no longer bound by the genophage, the Krogans are going to go on a rampage of conquest again". Wow, racist much? In all seriousness, although Wrex is stranded in the Sol system, he can still communicate with Tuchanka. Eve/Bakara, the shaman of the female clan and now a very important figure for the Krogan, remains on Tuchanka and is just as determined and wise a leader as Wrex. It's true that Wrex and Bakara together would have made the best leaders for the Krogan, and had the best chance of preventing the mistakes of the past from being repeated, but I think with just Bakara on Tuchanka (and pregnant with Wrex's child), there is still hope for the Krogan's future. (Note that depending on the player's actions, both Wrex and Bakara could be dead, in which case this point is moot and the Krogan are lacking for good leadership anyway).
- "The endings are all the same, they just change the color of an effect in the final cutscene." OK, point. The endings are not the same, in that if you think about the implications of your decision they are very different, but the last cutscene you actually see is very similar no matter what you choose. A bit disappointing, sure, but there's so much choice and variety in how the game as a whole unfolds that I'm not that pissed off about it. It'd be nice to see a longer denouement that illustrated more of the unique decisions that you made, but again, this isn't such a deal-breaker for me given the overall job that the game did in wrapping up those storylines.
- "WTF was up with the Normandy fleeing the battle ahead of the signal? And why were my squadmates on board?" This particular criticism is, I think, by far the most valid that anyone has given. The game never establishes why the Normandy is flying away from the Sol system with Joker frantically trying to stay ahead of the energy wave/signal. It sets up the Normandy's crash on an unnamed planet (pretty unlikely if you're just cruising through a random mass-relay conduit), which does give us the powerful visual of Joker & EDI together on the surface (at least in my ending), but it can also show squad members that were with you in London emerging from the Normandy. I do consider this to be a serious plot hole, as there's no explanation for how your squadmates made it back to the Normandy, or for why the Normandy was leaving the battle. That's not to say that no reasonable explanation was possible, but I can't see any hint to one. Honestly, if any part of the ending needs "fixing", it's this. It doesn't negate all the good implied stuff or "ruin" the series, but there really isn't enough context to explain it.
So, that's my take on ME3. Understanding the ending takes a little intellectual legwork, but all the pieces are there and I like the conclusions that I reached. The Normandy plot hole, in particular, is frustrating, but if you don't let yourself get hung up on that, you can appreciate that ME3 was actually a brilliant conclusion to one of the greatest sci-fi sagas in videogame history.