Another idea for an ending, without indoctrination theory, and thought up by the user phrizek. For the sake of reiteration and to show that it is a pretty damn good idea:
"So right after the assault on the Cerberus home base we learn that the Citadel has been retaken and is now closed up in orbit around Earth. The only way in is a beam of light somewhere in London. So Shepard and company must...But wait! That simply isn't true, is it? There is a back door onto the station, and we've known about it since ME1: The Conduit at Ilos.
So here is my proposal. After destroying Cronos base you are told about the current situation and are given an option. You could travel to the Sol system on the galaxy map and launch the final mission (Priority: Earth) just like we have now. The mission, the ending, and the consequences will remain unchanged. Or we could download a new Ilos DLC that will enable us to travel to Ilos on the galaxy map and if we choose this branch, will launch a completely different ending sequence (Priority: Ilos).
This ending will mirror the the end of the first game, providing a good bookend to the series, especially for long-time fans. The story could be that after the events of Mass Effect, the council secretly sent a regiment of troops and STG personnel under the guise of an archeological expedition to safeguard the conduit, lest it fall into the wrong hands and lead to another sneak attack on the station. After the Reapers capture the Citadel and park it in Earth orbit, they go after the conduit knowing it could be used to enter the station. Shepard recieves (or is told of by Hackett) a distress call from Ilos. At this point you can choose to go there and attempt to get on the Citadel via the conduit. When you arrive, you find the troops and Salarian STG holding off an attack by reaper forces. An STG captain tells you that their main force is split up and another group is holding steady at the conduit, ready to activate it as soon as Shepard gets there. He gives you the a vehicle (Mako or Hammerhead) and you must now fight your way through hordes of reaper uglies to the conduit, just as you did with Saren's geth at the end of ME1. Just before you reach the conduit, Harbinger shows up to stop you but the Normandy and some allied ships arrive in the nick of time and blow it away with their Thanix cannons, kind of like what we see in this trailer:
http://youtu.be/eBktyyaV9LY?t=2m35s
Now here is where things get interesting. As the mission progresses, the perspective changes from Shepard's squad to that of Admiral Hackett commanding the fleets trying to retake Earth, in much the same way ME1 had the perspective change from that of Shepard to the space battle for the Citadel going on outside. Only one major difference here: when the perspective changes, the player gains control of Admiral Hackett as he is guiding the allied fleet against the Reapers. This won't be full control or anything like Shepard, but you should get to control some dialogue options when Hackett is giving his rousing speech to the armada. The scene could take place in a command center type room with a large holographic readout of the battle. Here you could have some light RTS elements where you get to decide on some tactics and strategy with regards to how the battle plays out. War assets should come into play here and different cutscenes happen depending on how well you prepared. This perspective switching is done so you won't lose sight of the battle that is going on at Earth.
Shepard eventually reaches the conduit and is transported to the presidium, just like in the first game. This could be a really interesting mission as you are caught in the middle of the second battle of the citadel, as C-Sec forces and armed civilians are trying to hold back againt the Reaper horde now occupying the station. Gunfire and explosions are everywhere on the once pristine presidium as its occupants try to survive as best they can. Your war assets also come into play here, and whether you did the side missions to prepare the citadel forces has an effect on how well they are holding the station. If you prepared well enough, you could even meet up with Commander Bailey and tell him that you need to get to the council chambers to open up the citadel arms. If you didn't prepare well enough, the mood is darker, more bodies litter the floor, and the reaper forces have the station almost completely subdued. When you arrive at the council chambers, the Illusive Man would be waiting for you just like in the ending we already have. This could play out just like the Saren scene in ME1, and you can convince him that he is a traitor to humanity and he puts a bullet in his noggin.
Afterwards, Shepard opens up the arms, the Crucible docks and then it activates. We now learn that the purpose of the Crucible is to overload kinetic barriers, like an engineers Overload ability but on a massive scale. We learn that the blast has not only knocked out the Reaper's kinetic barriers (their major advantage) but the barriers of galactic armada as well. With no barriers on both sides, the final battle comes down to how well you prepared earlier in the game, how many war assets you acquired and how high your EMS is. As Shepard looks on, a massive battle rages with only two outcomes: extinction or survival. Either you prepared well enough and the Reapers lose out to the combined numbers of the galactic fleet, or you watch in horror as the reapers tear the last remnant of your armada apart.
Different factors related to how you prepared will determine who lives and who dies and we can get a range of victorious endings depending on how that plays out. We get a proper epilogue with all the characters who survived. If you did not prepare and lose everything, the game ends with a scene 50,000 years in the future where some other races have discovered Liara's time capsules and because of it, finally go on to defeat the reapers. They march into battle wearing N7 markings. Since Bioware is so hell bent on getting rid of the Mass Relays, if you get one of the good endings, one of the final scenes explains how galactic society allowed this catastrophe to happen because they got complacent and relied to much on the technology of the Citadel and the Mass Relays. They decide that they need to develop on their own. The races of the galaxy go back to their home systems. Shepard says goodbye to his friends and crew mates, and then goes to live with his LI (Rannoch, Thessia, Palaven, etc.). The occupants of the Citadel leave and the station is abandoned. In a "Last one out turn off the lights" type of scene, the lights on the Citadel wards begin to slowly turn off one by one until the station is covered in darkness. From knowledge gained by the Prothean VI, it is learned how the Citadel controls every Mass Relay in the galaxy. The final switch is turned off and all of the Relays in the galaxy go dark, unusable. To ensure that they cannot be activated again, the Citadel is driven into Jupiter by the alliance fleet, where it is wholly and utterly consumed. The game ends on a "we will meet each other again, when we are all ready" note, giving a sense of hope for a new, post-Reaper unified galaxy. The end.
The best thing about this idea is if you like the original ending, that is totally your option. Just choose to launch the end game from Earth instead of Ilos. For the rest of us, we get the ending we want in a totally optional way that doesn't detract from Bioware's original ending."
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I completely think something bigger is happening in this "ending" (I prefer to say cliffhanger), because it is difficult for me to belive that you, the Bioware team, would...
it'd be swell if you choose for him to repeat them. or even better, a little Q&A with crucible kid would've been nice. I had no flipping clue what controlling the reapers would really do or what mixing organics and synthetics would do.
