But as Season 3 approaches, Dr. Thompkins is back in the picture - with a new man at her side - and Baccarin is back on the set of the Fox drama.
The "Deadpool" actress joined journalists at Comic-Con International in San Diego to offer a hint at what's ahead following Lee's split from Gotham's hero cop.
How soon into the season do we get to see you appear again?
Morena Baccarin: Right away. I come in the first episode, and we're in very different places, Jim and Leslie. She's with somebody else, which he sees right away. They've got a long, uphill battle, and we'll see if they make it.
Is it someone we've seen?
New character: It's Falcone's son. I think I'm allowed to tell you all this. Nobody's stopping me. A thunderbolt hasn't struck me from the sky, yeah!
This new love interest is going to be very interesting because we've only ever seen Leslie with Jim. We've only ever seen their love story. And now there's something for him to work for. So it'll be ... it's exciting as an actor to play that conflict. He's certainly not a choir boy, so we'll see what happens with his life. It will not be easy. So they'll have something to work towards.
How different is this new relationship?
This is just the beginning. But I think when you go through a tragic, a traumatic event, you seek somebody that is more of a caretaker, or seems more level-headed or whatever. That's what he seems to be. Of course, it's "Gotham." Things change.
With a cast as big as this, do you get to interact with any new folks?
I hear that I will. I haven't yet, but I will.
With so much emphasis on the male characters in the show, as a female character, what would you like to see happen with Leslie?
Last year, because she was in service of Jim and trying to right his wrongs or start a family together, she ended up I think taking more of a passive role in Gotham, in general, and just really not having her own things going on. So it would be nice to see her side of the story a little bit, which we'll get with this new love interest and her new life.
What fun about this particular year, where you had a foot into both the Batman and X-Men universes?
I'm pinching myself every day. I don't know how I got so lucky to be able to be in both Marvel and DC universes and have it all be successful. It's been really fun. I can't wait to do more.
A second "Deadpool" film is already in the works. Have they been in contact with you about details?
No, I don't really know exactly what's going on. I've been told I will be in it. I don't know to what capacity or what they're planning. I'm dying to find out. Let me know what you hear!
"Gotham" returns Monday, Sept. 19, on Fox.