The fourth episode, too, where Sam convinces Gene to follow his principles, and they arrest Warren together. When Sam and Gene return to the station, they are met with applause.
Gene: Everyone here will be holding their heads a little bit higher tomorrow because of what you've done.
The end of series 1 episode 6, where Sam remembers a memory of his father he had as a child. It turns out the crime had nothing to do with the doctors pulling the plug — that moment of happiness in the face of adversity is what convinces them not to instead.
"And I didn't turn around, because I knew my dad was home..."
Any scene where Gene and Sam put aside their differences and unite for a common goal, really.
"Stay. Here. Forever."
"Okay. I will."
Gene going straight to Sam when he's been accused of murder.