In Danganronpa, how can a classroom trial be called if there are only 2 witnesses available?
Danganronpa V3 addresses this
Note: I am putting it as a spoiler even though it is presented to you before the first chapter.
In the most recent game, DRV3, A school regulation is created by Monokuma. stating:

 #6: If innocent students (hereinafter referred to as &quot;the spotless&quot;) continue to survive the class trials, the killing game will continue until only two students remain.

From this regulation, it seems the game will end immediately when only two students are alive. In the situation you presented, one of the final two will be the blackened. However, the regulation states &quot;two students&quot;, not &quot;two spotless students&quot;. This means that the game will end with two students, regardless of their blackened status.