After his recovery, Shoko takes him back to school for to meet up with everyone again. (At the school festival, of course. This is anime.)
And what we see, ultimately, is that Ishida has been suffering from some form of social anxiety. He can't look anyone in the eye.
Social interaction makes him sick to his stomach.
Nagatsuka tracks him down to pull him out of his shell.
His friends have been worried about him. They've been working on folding 1000 paper cranes (a traditional good luck/get well charm.)