Doggett leaves Dickhead and trails the kid, finding a room which he calls "the source of the contagion" -- the room where the leak originated. Water from the bay is trickling in, coating the walls and the floor. The kid splashes through the room, still gesturing for Doggett to follow. Scully looks at her map and tells Doggett that the kid appears to be leading him into an active line, about four hundred yards from an "access point." If he can get to that point, she tells him, she can get him out in roughly fifteen minutes. Doggett goes back to fetch Dickhead.
They lurch through the contaminated room, and out onto the main system, which Doggett notices has also been contaminated by the Evil Ocean Water. Scully sighs that they have bigger problems than that: there's a train heading right for them
Drums of Impending Doom. Doggett drops Dickhead to go investigate. The subway is, yes, heading right for him. Scully yells at Doggett to get off the tracks! Doggett yells that people on the train will get infected! Scully yells at him to save himself, man! Doggett ignores her, and gestures to the kid to hand him something, which he does. I can't tell what it is, thanks to the damned atmospheric lighting. Whatever it is, Doggett -- like some kind of twenty-first-century MacGyver -- in the space of, like, two seconds, manages to use it to create an electrical-type explosion between the water and the live third rail, and also somehow jumps out of the way of the oncoming train right in the nick of time.
In the control center, the monitor has gone out, and Scully freaks, obviously thinking that Doggett has been plowed down by the subway train. In a moment, he responds to her calls, although it takes a while for "the visual" to come back. Scully is noticeably relived. Doggett heaves giant breaths and stares at the hole in the ground created by his nifty explosion. He looks at the leak, and at his hands. The phosphoresce is gone. "Are you okay?" Scully asks. "You can only hope, Agent Scully," Doggett wryly comments, staring at the no-longer glowing water. Okay, I have no idea what just happened there.