An envelope (addressed to "Katsuragi Misato-sama") and a security card are the only things on the desk.
Shin-seiki: Interesting that he used the formal honorific "-sama" here; that's something that I never caught on to before…
Hexon.arq: To lighten the blow, I imagine.
Incisivis: So Shinji leaves without telling Misato to her face. Here I think Shinji's motivation is not fear of Misato (as it will be in episode #24), but a desire to "find himself". Shinji has recently had his first taste of active violence and wonders what it means for himself and his future, and needs to get away from the human world to determine that. I don't think Shinji gets any answers, though.
But leaving the message for Misato shows that Shinji does care to an extent, that he doesn't want to leave without saying something, which points to his redemptive potential. Also, "Misato-sama" may be his way of showing that he "respects" Misato enough to leave that message, or such a respectful honorific may be Shinji's way of asking for forgiveness.
OMF: It's just like Shinji. I'd wager the letter is an elaborate and breathtaking study in written apology, overflowing with deeply considered prose, and inscribed with intricate calligraphy.
Reichu:: "So, you thought you could be my surrogate mom, huh?
