1) IT doenst claim that the indoctrination begins at the moment when Harbringer hits you with the laser. Quite on the contrary, IT uses evidence of Sheppard being indoctrinated during all mass effect 3, or even earlier, to show that Sheppard is being indoctrinated since weeks, or even years. Just in ME3, all dreams are actually hallucinations of indoctrination. Some even claim that certain akward events back at ME1 show that you are contaminated with indoctrination since the point you touch the first beacon, but that is a little bit debated among IT followers. All agree that the dreams on ME3 show that Sheppard is being indoctrinated, slowly, through the whole ME3.



And you are right: how the hell did Sheppard survive the attack of Harbringer?. But it gets even more weird... Why, if you stay there without moving, Harbringer never attacks you?. Why (on the EC DLC), when you help your companion evacuate through the normandy (if your EMS is high), Harbringer doesnt take the chance to blow you into pieces along with the Normandy. Or (If your EMS is low) why does he first separate Sheppard from his company by throwing a tank in the way, and then deliberately uses its laser to kill your friends but doesnt kil you, even more, the laser comes from behind them, away from Sheppard, like if Harbringer is desperately trying to not hurt Sheppard. Without IT, this doesnt make much sense: Harbringer is trying to stop everyone from reaching the Citadel, and Sheppard, among all of them, is a serious threat inside the Citadel and handling the Crucible...



But what if Harbringer has other interests in Sheppard? well, some IT fans would claim that they want to indcotrinate Sheppard and that he is more usefull alive than dead, and thats why all of the above makes sense, and also why Harbringer's laser doesnt kill you. He simply gives you a hit strong enough to knock you out but not kill you. And he renders you unconsious, cause when we are sleep or uncounsious is when Reaper´s indoctrination becomes stronger. The Reapers desperately want to indoctrinate Sheppard, sadly one can only speculate on the reasons of why.