Final Fantasy has a long, proud tradition of protagonists aiding the villlains and/or doing great harm.

Cecil - Helped collect multiple crystals for Golbez, wiped out the Summoner Villge
Cloud - ...where to even start? I guess we'll just finish with the fact he gave the Black Materia to Sephiroth.
Squall - Took Rinoa into space thus freeing Adel
Zidane - Broke the seal to Terra and defeated Garland, allowing Kuja to hijack the Invincible and gain Trance

All these I know of and there might very well be more in FFV, VI, X or XII.

So, what other ways have our intrepid heroes screwed everyone?

And who takes the award for doing the most damage?