RulingRules Reference 1.7

If an ally is not discarded after being defeated by an enemy attack (for instance, it is returned to hand or shuffled…

Question

If an ally is not discarded after being defeated by an enemy attack (for instance, it is returned to hand or shuffled into a player’s deck), does it go under Operation Zero Tolerance?

Answer

Yes. Operation Zero Tolerance does not specify where to find the defeated ally when it resolves, so it is placed under Operation Zero Tolerance, regardless of where it ended up.

— Rules Reference 1.7