Well, the Angel was defeated, and while Rei and Kaworu have suffered severe injury to their AT fields, it hasn't outright crippled them, to the extent that Asuka suffered originally. It's going to be nerve-wracking, to wait and see if Shinji can manage to keep his mouth shut when he's confronted by his father, and if Rei can recover and keep up appearances.
I fear Shinji keeping the letter might cause trouble, though maybe keeping it in his plugsuit will make unreadable by morning. Perspiration, you know. If Gendo does find out about the contents of the letter, he'll have enough ammunition to seriously put the arrangements regarding the Second and Third Children in question, and Misato's guardianship of them. Even maybe her capacity as Tactical Commander. One letter, however spicy, isn't necessarily
proof that Shinji and Asuka are having sex (and lacking a hymen isn't either, medically speaking), but Gendo doesn't need proof unfortunately to make the administrative decision to have the pilots housed seperately elsewhere. Shinji apparently developing a relationship might just be a trigger all of its own, since Gendo is incapable of moving past his relationship with Yui, and it's all a childish waste and futile anyway, with the End of the World approaching.
Gendo might decide that Rei II is simply too great of a risk as well, if her recovery might take too long, or if she simply can't keep up the act around him, now that she has experienced real "human" (and angel) interaction unfiltered.
On a different note, am I the only one dreading Asuka's reaction to seeing Rei going through withdrawal again after being in Ritsuko's care?
Rei shouldn't have to experience withdrawal again like that. As long as Ritsuko remains in charge of Rei's health, she can hopefully manage the detoxification without as much discomfort (and risk) as Rei's initial "cold turkey" trip.
The End is indeed soon at hand, just a matter of weeks or a month, probably not two... The next Angel is one of the nastiest as well, with its ability to infiltrate the EVAs. Gendo will be adamant that Unit 01
not repeat not be put at risk
again. period. Hmm, I know UNIT 01 rejected the DP system, but has Unit 01 rejected Rei completely? If not, maybe Gendo will try to use Rei instead of Shinji. With Yui "aware", and Rei "awakened", there might be the chance for a very interesting interaction between Rei who loves Shinji and could be technically Yui's daughter, to set up things for the climax at 3I.