Of course he was upset, but that didn't stop him from helping out others! [Nagito seems maybe a little too willing to gush over Makoto.] Naegi-sama even took the time to help out someone as wretched as me! He's the Super High School Level Hope, so it only follows that a distressing situation like the Crossing would only be a minor setback for him.

[Nagito's opinions of Makoto may not be completely objective here.]