Dark Phoniex Saga, followed by the Mutant X,"Proteus," story arch. Nigga Proteus literally had Logan cowering like a bitch. Cyclops had to get Logan to go into berserker mode to get Logan out of that shit. In the couse of taking mad shit to Logan, Scott put his life at risk. The story was epic because Claremont's skill at writing team book were at their peak.
It took the combined efforts of Logan, Jeanie, Ororo, Pietor, Kurt, Scott, Alex, & Lorna to subdue Proteus. One of the cooler parts of the story was when Logan admitted the Scott was a good leader and he admired him as a man.