Sorry about that, I just typed fast. Here you go
This is how I believe shepard got indoctrinated.
After the events of ME1 harbinger (who I assume is the Alpha reaper, being the largest and oldest - check codex) realizes that shep is a massive threat to the reapers because of his ability to rally people to his cause and if he was able to rally the entire galaxy then the reapers plans for consuming all advance life in the galaxy would be doomed to fail. So first he sends the collectors to kill shep but did not figure on Cerberus (who i believe that the IM is not indoctrinated at this point, That happens before ME3) resurrecting shep and helping him.
Then after a number of confrontations with shep while controlling the collectors, harbinger realizes that killing him is not the way and so he must be indoctrinated. Now shep has had exposure to the reapers and their technology(object rho where he got a big does of reaper magic and could hear harbinger in his head), but at this point he has had 3 massive victories(one cost 300,000 batarians) against them and his will and resolve are too strong for indoctrination to work. But the ground work has been laid with the connection that harbinger made.
No skip to the start of ME3 and shep sees a boy playing in his garden, this is the last happy image that shep will see before everything goes to hell. Also harbinger is leading the attack on earth( and we know that he can connect with someone over a long distance, like the collectors while in darkspace.) and during the attack shep sees that boy in a vent after hearing a loud bang(I believe that from this point the boy is dead and this is the hallucination that harbinger creates.
The boy tells him that he can not save him and then disappears suddenly and was very quiet about it. Also note that anderson did not see or hear the boy. The we get to the killer moment. Shep sees the boy board a shuttle only to be killed by a reaper. The guilt shep feels is enough for a crack to show in his will and resolve and that is enough for harbinger to keep picking at during the course of the game.
And this is with the nightmares. The first one has shep chasing the boy until he sees the boy burn in front of him. The second nightmare(which happens after shep loses both victnas's son and Mordin, both of which have an effect on him) is the same as the first but now the forest is littered with dark figures, I thought at first these signified the dead, but I think it shows instead the reaper presence in his mind Also he hears voices in all three dreams and the voice get louder in each. The third and final dream( which occurs after shep and co were defeated by cerberus at Thessia) again is the same as the first two but with more black figures in it and also ends with the boy and a version of shep smiling back at him while burning. I think this means that the connection with shep is strong now and his resolve has fractured now allowing indoctrination to take place.
Which happens on earth at the conduit with harbinger right in front of him. So after the attack shep seems to have survived, although you hear on the radio that no one did, and heads up to the citadel where anderson who looks alittle hurt but not to the extent that a reaper laser would cause( look at shep for that) and then the IM turns up out of the blue. Now this I believe is the battle going on inside his mind, with anderson representing the side of shep resisting indoctrination and the IM who represents the reapers. Once shep gets the IM out of the way. It seems that he has won and anderson dies.
But this is to lead shep into a false sense of security because the final test is the catalyst. Which appears as the boy that caused shep to feel guilty and question himself. Also the catalyst(star child lol) also has both femsehp and male shep voices mixed with his own.
And he tells you the reapers plan but also gives hope in three options. The first is the one that shep should choose but it is in renegade red and the catalyst gives you reasons not to go through with it.(The geth would die, EDI would die and he would probably die, plus anderson is shown in the clip which is weird for a renegade choice) so then comes the option to control the reapers, which is the IM's choice and shep is told that everyone will live but he will die and reapers would also live and sot to go down this path would mean that indoctrination is successful.
Then there is the third choice which is similar to the control option and so the reapers would win again. So shep instead goes for destroy option, which means that the indoctrination failed and shep wakes up in the rubble in london where he was left. And the so the story would carry on in an upcoming DLC.
Also I think that the crucible is a reaper trojan horse to give the galaxy hope that they destroy the reapers but really all it does is take the galaxy's attention from the real target which is.......Harbinger. Kill him and the reapers fall.
And the bits with the relays blowing and the normandy, well since it is a dream then they would not make sense(because when idd our dreams ever make sense). But they maybe in there as a repercussion for the choice that shep makes (the relays blowing up.) and the normandy crashing on a planet(show shep that his friends who did not go on the run to the conduit with him did survive.)
And the bit right at the end with the old man and kid. "Tell me and another story about the shepard"
"Ok one more story" I think is a foreshadow to the finale DLC.
Thats what I think anyway, please let me know what you guys think.
os, is that any better?