Right after Gonta's execution, Kokichi starts planning ahead and tries to figure out who the mastermind is. Stumbling upon some disturbing evidence of one of the few people he put even the slightest amount of trust in.
This is one of the three paths of The Boy With The Blank Stare. In this route Ouma desires revenge to those who wronged him in his time of need and searches for the culprit who broke him and massacred countless others. On the sidelines to Ouma's new outlook on life Saihara is conflicted in trying to figure out what he can do to stop Ouma and finally save him from his past.
Make sure to read The Boy With The Blank Stare before this in order to understand as it will have multiple references to it and spoilers.