Series opens on Kate Keene diving deep to retrieve a key to the handcuffs that are locked around her ankles. When she returns to the surface, she finds the opening in the ice has been blocked. As her brain flashes to the night her mother and sister died, she finds the will to break through the ice. Her trainer is glad she survives but criticizes the time it took her.
Voiceover explains that Batman has been missing for three years and the residents have run out of hope. Kate's father, Jacob has started a security firm to keep people safe. There is a gala being held, hosted by his new wife, Catherine, for the official shutting off of the Bat Signal.
Alice strikes, killing the GCPD officers in charge of shutting of the beacons and then kidnapping one of Jacob's Crow agents, Sophie Moore.
Kate's stepsister, Mary, calls to let her know that Sophie's been taken. In flashback, it is revealed that Kate and Sophie were lovers in military school.
Kate returns to Gotham but her father dismisses her attempts to help the Crows find Sophie. In flashback, Kate and Sophie are caught in a romantic moment by their commanding officer at the Academy.
Kate breaks into the boarded-up Wayne Enterprises building and gets caught by Luke Fox. She outmaneuvers him and finds footage of Sophie's abduction.
Returning to her father's home with the footage, Kate is surprised by a welcome back party. Mary confides that she knew Kate and Sophie had had a relationship because she found some pictures.
In flashback, Kate and Sophie suffer the fallout of breaking the military academy's anti-gay code of conduct. Kate refuses to sign the official denial of her homosexuality but Sophie does and the two part ways.
Reviewing the footage with the Crows, Kate realize Alice's crew is at the Burnside Orphanage. She beats the Crows there and takes out several of Alice's henchmen before being knocked out.
She wakes up to Alice playing with a butterfly knife. Alice gives her a message for Jacob, that she wants to strip him of his power. She also tells Kate that Sophie is the daughter Jacob always wanted, that he doesn't want Kate around.
Kate wakes up in an underground clinic where Mary is the attending doctor. Sewn up, she heads back to the Crows' headquarters and confronts her father about how he pushes her away.
She heads back to Wayne Industries and interrogates Fox about Bruce's whereabouts. Looking around, she notices Martha Wayne's pearl necklace container has been moved. Putting it back in place, she discovers the entrance to the Bat Cave.
Luke Fox meets her down below and explains that Bruce was haunted by the fact he didn't save her mother and sister the night they died. Kate decides that she will become the new vigilante protector of Gotham.
Gotham's Movie in the Park is underway with Jacob's Crows securing the area. He doesn't like the look of a building under construction nearby and asks which agent is covering it and is told it's Dodgson. Meanwhile, Sophie is bound and gagged on one of the upper storeys with Alice and some henchmen when Dodgson comes in and kisses Alice.
Alice contacts Jacob and lets him know there's a truck full of explosives parked next to the crowd watching the movie. If he does anything to alert the crowd, she'll detonate it. Meanwhile, she has Sophie out on a plank and wants Jacob to choose between saving his favorite agent or the city.
Suddenly, Alice's henchmen start being picked off, one by one. A Batman-like silhouette appears. Alice punctures a hole in a water drum balanced against Sophie's plank. Alice and Batwoman fight. Alice drops the detonator and Batwoman knocks it over the edge and out of her reach. Sophie's plank falls and Batwoman dives after her and helps break her fall onto the bed in a watchperson's office. There's an intimate moment shared between them before Batwoman gets up, leaves the building and shoots a grappling hook back up to the floor she fought Alice on, leaving Sophie to be found by Jacob and his men.
Alice is gone when Batwoman arrives but she's left a butterfly knife which Batwoman takes. Standing at the edge of the building, Gotham residents catch sight of what looks like Batman and get excited about his return.
As Kate watches from an observation room, Jacob gives the Crows the mission to track down Alice and Dodgson. Sophie realizes she was rescued by a woman then spots Kate leaving the observation room. Kate and Sophie run into each other at the coffee machine where Sophie's husband, Tyler, finds them.
Jacob returns home to find Kate and she confronts him about his plans for her. He comes clean and admits he never wanted her to be in danger but that he's willing to let her be a part of the Crows if she wants now.
In the Batcave, Kate writes to Bruce about how she's found freedom in being Batwoman. Luke joins her and mentions that Bruce never stopped looking for Beth's body. Kate wonders why he never did and then looks at Alice knife. In the hilt she sees a gemstone that matches the pendant Beth wore. She realizes Alice is Beth. In her lair, Alice looks at the Polaroid of Beth and Kate taken just before the accident that killed their mother and swears that she and Kate will be united and rule Gotham together.