The Corruption won when it attacked The Institute in Season 1.
Sure, Jane Prentiss and the worm’s were destroyed, but the lingering effects of the attack causes toxicity between every relationship in The Institute.
Jon becomes paranoid in the way that strains his relationship with Martin, destroys his relationship with Tim, and fundamentally effects every relationship he has for the rest of the series.
Jon’s paranoia also end’s up breaking Tim and Martin’s friendship, with Martin being being dismissive of Tim’s feelings in favor of Jon’s, and Tim being too caught up in his anger to prioritize the feelings of anyone else.
Sasha get’s replaced and Not! Sasha end’s up dealing the final blow to all the problem’s the cast is already having. They add fuel to Jon’s paranoia fire as he knows something is wrong but can’t place it. They put Martin in a bad place by putting him in the middle of Jon and Tim’s heightened emotion. And they start pulling away from Tim, and when their identity is revealed, that destroy Tim’s trust in other’s completely.
The events of the corruption attack on The Institute end up leaving things…well, corrupted. It breaks multiple relationships and changes Tim and Jon for the worst, while also causing a few of Martin’s more negative traits to be on display. So while The Corruption may not have won the battle, it won the war, and it’s honestly devastating that the first attack the character’s go through is the one that end’s up leaving behind the rot.