[Warning: This story contains spoilers from Tuesday's season two finale of NBC's The Blacklist.]

Liz (Megan Boone) is finally learning more about the night of the fire on The Blacklist.

The NBC drama closed out its second season Thursday with the FBI agent shooting and killing Tom Connolly (Reed Birney) after confronting him for poisoning Cooper (Harry Lennix) and framing her for murder. As Connolly dies, Liz flashes back to the night of the fire and remembers shooting her father years ago as her parents were fighting. The episode ends with Red (James Spader) and Liz on the lam from the FBI.

Executive producer Jon Bokenkamp tells The Hollywood Reporter that the episode's conclusion had been in the works for the duration of the show's run. "The image of Liz's wanted poster going up next to Reddington's wanted poster is something we've talked about for a long time and one of those signpost moments in the series that we knew we wanted to hit," he says.

With the episode's "devastating" turn of events, Bokenkamp says that Liz's "line of good and bad has become blurred," as the finale "hardens her in ways and makes her more jaded and careful and really more like Reddington in a lot of ways."

"Red is heartbroken that, [despite] everything he's tried to do in this season to protect her from this horrible truth, she has discovered it," Bokenkamp explains, adding that the new season will see him continuing to struggle with this sense of having failed Liz. "[This storyline] opens and takes us into a new chapter where she is no longer just an FBI agent — they have a real journey that they're about to go on. They're entering the third season as fugitives."

One storyline that will be central to the third season is Liz and Ressler's (Diego Klattenhoff) dynamic, as he is tasked with hunting Liz down after having grown to respect her. The coming episodes will see a "complete shift between those two characters," Bokenkamp promises.

Another twist in the finale involved Liz going to Tom (Ryan Eggold) for support and then sleeping with him, although she ultimately turned down his offer to leave with him in his boat. By the close of the episode, Tom had disappeared.

"On a certain level, Liz turning to Tom is a desire to escape everything about herself and become something entirely new," the showrunner says. "That relationship is incredibly dysfunctional. I don't think there's much that's healthy about it, but I think both characters are grappling with big questions of identity and questions of wanting to become something that they're not."

For the time being, the night of passion doesn't necessarily portend a rosy future for the pair. "[Their hook-up] is a moment of honesty between those two characters; it doesn't mean that either of them believe that they're going to move into a home with a picket fence," Bokenkamp acknowledges. "They both recognize that will never happen."

What did you think of the finale and Liz's revelation? Sound off in the comments!

Email: Ryan.Gajewski@THR.com

Twitter: @_RyanGajewski