James Isn't Actually Dead
Season one left us with the grim notion that James was dead after we heard a gunshot, accompanied by a scene of him spilling blood onto the sandy shore of the beach he and Alyssa were hiding out on. In season two, we learn from James himself that he's still alive. He gives a voiceover saying, "It was a fitting end, a doomed love story. A perfect tragedy. And then I didn't die."
After he survived the gunshot and spent months recovering in the hospital, he then got probation after the judge ruled the professor's murder an act of self-defense. The only downside to all of this? Alyssa's mom forced James to write a letter explaining that he never wanted to see Alyssa again. Watching James write the letter was as painful as it was for him to write it, knowing that he and Alyssa would never really stop loving each other.