Let me guess this straight. He unintentionally caused Third Impact by trying to save Ayanami. But, he did so because someone encouraged him to do so.
IIRC, he didn't want to deal with EVA anymore and someone else could do it instead. He still wants to help out Ayanami but still ...
Anyway, Ayanami stuck in EVA-01and most of humanity died or became something worse. when Shinji woke up, everyone in the new organization that got him are douches (justified but still). He has a choker on his neck that will detonate whenever the Captain feels like it. Obviously, as any prisoner would do, he would get out ASAP even though it's the baddies that got him. The baddies are smart enough to actually tell him the truth to the extent that he trusted them (Kaworu at least) after realizing that NERV (probably) wants him to finish the destruction he started.
In the end, the baddies succeeded with their plan and nobody still won't leave Shinji alone no matter what how much he's against it.

I'm fine with the way Shinji acted (it's either what he did or suicide). All in NERV and SEELE except Rei clone are fine. Rei clone is almost fine (WTF she suddenly had some conscience in the last minute and GTFO when she should be almost completely stoic).
As for the rest, talking with no threats of violence still works and is best when it comes to Shinji.

Evangelion really shines with its characters leading the plot but this ... the opposing side might as well have not existed and the ending probably would still be the same. Heck, Kaworu might have been able to explain everything to Shinji on time and the entire plan would have failed because there's no outside pressure to force Shinji to quickly pull out the spears. Shinji hesitates all the time (especially after the reveal) so if he's not pressure to quickly make a choice, he can be talked out of it.

Anyway, just as planned and hope Shinji can finally get his peace because he desperately needs it restore his sanity. If he loses it, either end of the world or his replacement does it if Gendo has one prepared.