In order to get the Shepard waking up scene you need to do: A.) Get either 4,000 EMS and higher with a full paragon/full renegade and ALSO make all the top left choices each time you see TIM (so Paragon choices whenever they pop up). If you pick Paragon, you must choose Paragon every time you see TIM otherwise it will not work. It does not work with Renegade. If you use Renegade you can forget this option. It mirrors that of the encounters with Saren from ME1.
B.) Otherwise you can just get 5,000 EMS. Either option will work.
In any event from either of these options, doing so will give you the chance to delay Anderson's death and to mirror TIM scene like that of Saren. Afterwards, during the star child scene, you must pick the 'destroy' option in order for it to work.
If you want the added scene at the end of the game credits, you need to either import a ME2 game save or play a new game +.
As for the ending of the game, at first I was pissed. Then I went back and replayed it again. And then I sort of liked it. Let me say this I still feel it was a total cop out how Bioware ended the series and it was not what I expected to happen at all but it does make sense.
The indoctrination theory seems to be the most logical choice for many reasons. But we all know they're gonna have some sort of DLC but yeah... the entire ending was indoctrination.
There is evidence to support this theory. Here is what I came up with.
1. After Harbinger uses his death ray and hits you with it, everything goes black. When you come to the first thing you should notice is a pitch shriek, sorta like the asari reapers, except slightly different and you can see Harbinger flying away. The shriek is a sign of indoctrination taking place. The farmers on Eden Prime talk about this as one of the symptoms they felt when they encountered Sovereign. It's also in the codex I believe for either ME1/ME2.
2. Shepard survives a death ray blast? Come on, even Chris Redfield couldn't pull that off. You witnessed it first hand when you ran towards that beacon. The damn ray destroys ships the second that beam hits it. There is no way Shepard should be able to stand up, even if he is all bloody and beaten, and continue further.
3. When you get control of the character you'll notice you have infinite bullets, you lost all your armor, and if you turn around, you don't see anyone else or anything for that matter. If you listen carefully or turn on the text subs during the very beginning you can hear something that sounds far off in the distance, chatter over a radio between Alliance operatives. They say that NO ONE SURVIVED the charge towards the beacon and ordered a full retreat.
4. Upon entering the beacon beam and transporting to the Citadel you hear Anderson speak to you. He says he followed in behind you, yet if you were outside and turned around, there is no one behind you. When you enter he says he got transported to a different tunnel.
5. After passing through the keeper tunnel with the human bodies on both side and entering the next room you can make out "1M1" on the left side before the bridge crossing and on the opposite side it has "1M1" EXCEPT IT IS BACKWARDS. Dreams are usually interpretation to be mirrored at times.
6. When you see Anderson at the controls, he's being controlled yet he has not even gone through indoctrination, and if he was indoctrinated he is the quickest to be turned in the MEverse.
7. TIM magically pops up behind Shepard. And he's been indoctrinated. The entire scene MIRRORS almost directly that of Saren from ME1. If you do what I said above, TIM even puts the gun to his own head and pulls the trigger just like Saren. Also take note of the black mist swirls around the border of the screen..... more signs of indoctrination.
8. After Anderson dies and Shepard goes to the top of the Citadel where there is no protection or gravity, he can breathe perfectly. Yes, he can breathe and speak without a helmet or anything to the star child.
9. The star child is a reaper A.I. The child you saw in the beginning of the game was never there. Don't believe me? Go back and play the first mission again. No one else sees the kid. You need further proof? Right before Anderson tells you to shoot the husks when you first see them, before that scene, look out to the right and you can see the child running into the building and the husks never touch him. When you see the child in the vent, only Shepard sees him. When Anderson snaps him out of it, the child is gone, and if you listen carefully, you can hear a growl. The growl from the vent is another sign of indoctrination. I forgot what character said it but they specifically said they could sometimes hear growling. And then you see the child get on the transport and yet no one even looks at the kid except Shepard.
10. The dream sequences was Shepard attempting to cope with finding the child because he feels guilty and responsible for his 'death'. Notice whenever you get close to the kid, the reaper alarm goes off. And when you see Shepard holding the boy in the last sequence, they both burn in flames. It was a foreshadowing that accepting the kid would bring humanity to doom.
11. If you do everything right in the game you'll get three options and the full scene will play out. The full scene goes that the boy is what controls the reapers. The truth is that the boy is the illusion of a reaper A.I. signal for Shepard to understand. The child is not to be trusted. No child in a sci-fi series is ever to be trusted, especially when it's machine.
12. The star child gives you three choices with the first being the default and the most obvious; destroy. It is what you, the gamer and your character, set out to do. Destroy the Reapers and save the galaxy. The star child obviously is going to get this choice out of the way so that when he tells you the other choices, the first choice in your human head becomes more distant and seems worse. Whenever someone gives you a choice of more then two, the first is usually the crappiest. So the destroy option is given and the star child tells you that it will destroy all synthetic life including the geth and most likely kill you. Shepard DOUBTS him about it. You see a weird flash of Anderson shooting the device to give you the destroy option. Anderson, a well developed embodiment of paragon, is doing something to destroy which is adapted as bad. Red is renegade as we've grown custom to throughout the series.
13. The next choice is CONTROL. You see a flash and TIM is controlling the reapers. The star child tells you that you will die but you will be able to control the reapers. The color associated with this is blue for paragon. Paragon is always the virtue one. However you saw TIM and you know he is anything but Paragon. Controlling the reapers is not possible and you will be indoctrinated.
14. The final choice is SYNTHESIS. The star child says this option was not available in previous cycles and recommends this one. If you notice, you'll catch the child in lies especially when he says control is better but then says this is now the best choice. Synthesis will merge both organic and synthetic life together. This is exactly what the Reapers wanted to do with the humans. This choice is the human being ascended to a higher form and becoming a nation in the reapers.
15. You see Joker escaping through a mass relay and somehow he magically picked up your love interest who was down on Earth. So magically he flew down to Earth somehow, collected your buddies, and managed to fly away from the Reapers before the Crucible went off. Doesn't make sense but then again it's not real.
16. The name crucible can be defined as being tested.
The entire ending, from the moment you wake up and enter the citadel, was a test. You fought all species of the galaxy and managed to take on the reapers. You have reaper technology in your body from the Lazarus Project and you came across them before. Anything that stays too long within reaper technology will eventually feel the signal and strength of them. Shepard is no different. It eventually happened. The entire sequence was the struggle from Harbinger attempting to indoctrinate both the character, and you, as the gamer. It's why the choices and the colors didn't add up. The reapers would not associate destroy with blue but with red to trick you. You were being indoctrinated. If you chose Destroy which is the destruction of synthetic life, you and Shepard break free of indoctrination, hence the scene after the Joker crashing on a planet plays out. You find Shepard back in London in the rubble and he takes a deep breath. This is him waking up after the death beam hitting him. He never encountered TIM, he never made it to the Citadel, and he did not yet destroy the Reapers.
The scene after the credits suggests that humans somehow found a way and won the war against the Reapers. It's never specified what happened to Shepard or who survived but the overall point was that humanity won and the Reapers were gone forever and that whenever that scene takes place, the cycle has not yet repeated itself.
I hope that helps some of you who felt screwed by the ending. Trust me, I am alongside with you. I didn't like the ending and still feel like I was robbed of something that should've been more but hopefully this theory helps some of your anger into the inevitable DLC extended ending...
