Mark's Final Battle with Graham: he confronts Edwina and makes herjoin their side, he manages to take photos of evidence about Graham trying to cover up the failures of his experiments and made-up results while Graham tries to beat him up, easily rebuffing his confident "why would they believe you?" by spelling these out to him, topped with "why wouldn't they believe us?", as well as spelling out the danger his career is in when he haughtily refuses being bossed around by a student because he is a renowned scientist. After breaking through his overconfident obliviousness of the danger he is in, Mark blackmails him into dropping all charges against Alex, and Ian offhandedly adds: "oh, and make sure Edwina gets another advisor". Because he saw her always drop a penny into the donation box in the cafeteria.
If Mark's friendship with Penny is doing well by the end, and if his grades are high enough, he goes into business with her when one of her apps makes it big. Even more awesome if you've romanced Phil, as his path includes a scene earlier where Penny tries to talk to an established app designer and gets rudely brushed off.