Season Three episode "The Search": Malloy takes off after a robbery suspect on his own. During the chase, he loses control of the car and goes off the side of the road into a wooded area. He's knocked unconscious, then wakes up with a broken leg and internal injuries. The radio's crapping out, which was foreshadowed earlier in the show when Reed had to keep repeating broadcasts. Malloy cuts a seatbelt and braces his leg with a shotgun. A search chopper comes by but he can't open the trunk to get to the highway flares and shooting his pistol doesn't draw attention. Later, a man comes out of the woods but it turns out he's a criminal from a different crime who's been hiding out there for a week and doesn't want to be found. He yanks the mike out of the radio and leaves Malloy to die. Hearing that Reed is searching near his area, he takes the split wires from the mike and the radio and starts signaling in morse code. Reed hears it and asks Malloy to signal once for yes and twice for no. The signals lead Reed to Malloy's location.
The two-part series finale, "Something Worth Dying For," sees Jim crawling out into the middle of a firefight in a drug dealer's house to grab a wounded, unconscious Pete and drag him to safety. Jim is subsequently awarded the Medal of Valor, one of the highest honors bestowed by the department.