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Alex confronting Michael when he thinks that he's cheating on Maria, even though Michael could beat the crap out of him even without his powers. When it turns out that Courtney is at his apartment, he punches Michael.
In "Independence Day", Michael is being physically abused by his foster father. After running away from Max and Isabel's attempts to help, he winds up standing outside Maria's window in the rain, and she lets him in and comforts him as he cries.
Maria: Shh, it's okay. You don't have to tell me, it's okay.
The ending to "Summer of '47" with Michael telling Captain Carver that he'd saved his life following the Roswell Incident and revealing his powers. Then they hug. Michael then goes to Liz and Maria and apologizes for what a jerk he's been and admits that he owes them for all they've done for him.