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He certainly got abused more than he was used to...but if fatigue is the argument...then it didn't start in September...it started in July when his HR rate jumped and his BB rate started its climb...which means he'll probably NEVER have the arm strength to maintain his 1H results for a whole season...he's too far away from reaching that.
Morrow is a wildcard...as I've opined elsewhere..the correct answer with him is to pair him with another starting pitcher and assume that both of them can get you 15-20 starts rather than expecting Morrow to get you 35.