Been so many replies, let me quote my original post that I'm replying to so the responses make sense.
Hmmm. I had a thought. We're told in Arrival that Kenson's indoctrination involved breaking down her will by torturing her over her past failures and mistakes. This is also how Shepard is indoctrinated for the most part. They keep harping on some damn kid that probably never existed to begin with.
People that didn't screw anything up too badly probably don't know this but you can end up having to face 3 former squad members. Jack, Legion, and Morinth. The first two are at Cronos Station and the last is in London. I think these appearances may be the same thing; the Reapers are torturing Shepard over terrible mistakes. All three of these encounters are past the Point of No Return meaning they're all highly suspect as to whether they were ever more than in Shepard's head, and none of the three make much sense when you think about it.
If Jack was alive at the start of ME3 but you didn't bother to save her and the kids at Grissom. She'll appear as a phantom with a name and she screams her usual battle phrases. "I will destroy you!" and the like. Cerberus was trying to study the potential of biotics for humans with her, that was the entire point originally. Why would they turn her into a generic phantom that they've already got armies of? That would be like finding the cure for cancer and then, instead of studying it, drinking it because it tastes great. Hell, the only reason we know it's Jack is because of her screaming her catchphrases, but have you ever seen another phantom (or any indoctrinated Cerberus troop for that matter) that retained its original mind after reprogramming?
Legion will appear shortly before the Kei Leng fight if I remember right. He's basically a nemesis. Same deal as Jack: they wanted Legion because he's the only in-tact geth they've ever had a chance to study. Why the hell would they take an invaluable research project and throw it away to create one more of a random trooper they have hordes of? It makes less than no sense. But it would make great sense if the purpose was to torment Shepard over giving the geth to Cerberus. That geth seemed to be an ally but Shepard refused to believe it and gave him to, and I'm quoting BioWare's debug script in ME2 here, "space (censored word for national socialist)." Come to find out the geth, aside from a fringe faction, are innocent victims having been betrayed and attacked by organics for no fault of their own time and again. And one of those times being at Shepard's ignorant hands. Perfect guilt trip material.
Morinth. If you killed Samara and spared Morinth, what the hell is wrong with you! ... Sorry, I just--no seriously, what were you thinking! ... *deep breath* Sorry, I'll try to restrain myself. Okay, so Morinth sends Shepard a goodbye e-mail at the beginning of the game is not heard from again until showing up in London. As a banshee. There's no dialogue as with Jack, there's literally no way you could possibly know that was Morinth except because the target indicator lists her name. How does Shepard know that's Morinth? And out of the millions of banshees that the Reapers have, she's one of the few on London that ends up battling Shepard? What exactly are the odds of that? The one ardat-yakshi that Shepard is responsible for, one who's extremely talented at going underground and hiding when the **** hits the fan, gets caught and winds up as one of the 0.01% of banshees that Shepard faces.
Now then...
HagarIshay wrote...
@Rifneno
Sorry to jump in there, just wanted to argue
The squadmates seem to also see the phantom is Jack. Even if your squadmates can also be in the process of indoctrination, does that mean they will all see the same hallucination?
IT has a lot of variations. I'm personally of the belief that Shepard never woke up from the third dream. Everything past it is completely in his head. There's a lot of disagreement here on when the hallucinations begin. Some think only after Harbinger's beam, some at the shuttle crash, some at the third dream, a few even go back to the bench hitting Shepard in the head in Vancouver, meaning the whole game was in his head.
byne wrote...
My renegade Shep spared Morinth because Samara had already stated that if I did things that were against her code, she would kill me when her oath expired. Morinth is less likely to kill me unless I'm extremely stupid, plus my Shep viewed her as less of a threat than Samara if she ever had to fight either of them at any point.
Meh. I always see Renegade Shepard as a bastard, not a coward. Personal safety is never high on Shepard's concerns no matter what your decisions are. Doesn't make any sense for Shepard to be going through the Omega-4 relay but killing an asari because he's afraid she'll try to kill him after helping. Besides which, Samara said she
may have to kill Shepard is Shepard makes
her do anything extremely dishonorable while under the oath. It was if you force her to betray her own beliefs by abusing her oath, not if you exercise different ones yourself.
paxxon wrote...
I fully agree. Those are the consequences of his actions. What did he expect? That they would come and thank him with wide smiles on their faces (or happy beeps from Legion).
And yet, after 3 games we only start fighting reprogramed former allies at a point where reality becomes highly suspect? That's a hell of a coincidence.
Though Cronos Station is fishy too. HellishFiend found an unsecured hull breach and a door leading to open space there. The door is such a big weirdness that it brings to mind the inconsistencies that are usually associated with dreaming.
I found that.

And there's more than one of those "hallways to nothing". Moreover, there's no good transition point if all of London was hallucination but Cronos Station was real. The shuttle crash happens long after most of the London weirdness. Whereas the third dream is an excellent transition point. IMO, CS and London are both fake. They only slowly made it more and more obvious that it's a hallucination so as to not spoil the surprise but also to make it so the casual observer gets it. Sanctuary has no documented weirdness. CS has some weirdness. London is really weird. After Harby's beam it's straight jacket material.
Big Bad wrote...
I actually kinda disagree about that. Shepherd may have to make all tbe tough decisions herself, but as far as I can recall she always has friends backing her up (ok, not during Arrival, but that's just an exception)...except during the ending of ME3.
Arrival pissed me off for that very reason.
Shepard: No problem, sir. I've got an excellent team.
Hackett: No team, Shepard. You have to do this alone. I don't want them spotting intruders and executing her.
Shepard: That won't be a problem, sir. Thane and Kasumi could sneak into a Reaper without it noticing.
Hackett: *sigh* Look Shepard, I'll level with you. We didn't bring back their voice actors for this.
Shepard: What? ... Well, okay. I can take Legion then, right? He's a computerized voice.
Hackett: No, his VA is a guy named D.C. Douglas. They just run it through an audio filter to make it sound computerized.
Shepard: ****.
Raistlin Majare 1992 wrote...
Exactly, Shepard is good, no the best. But he dident get to where he was alone. The mere fact that ME2 focuses on gathering a team shows this more than anything. He may be the best, but some things even he cant do alone.
Ask any hardcore Star Trek fan, there's some thing you don't want to have to do alone all the time.
... I'm sorry, I'll stop now.