I've encountered a spaceship that stated that I have a virus.
I've sent an Engi to talk with them, he disappeared, we had a fight.
After the fight he returned 'improved':
It looks to good to be true, so – is there a catch later on? or is it part of a quest?
Best Answer
Nope - no catch, at this point he's just a regular crew member (albeit a very skilled one.) He will behave as any other Engi crew would, and will stay with you until your victory / demise.
Source: FTL Wikia, personal gameplay