This season is set three days after the death of William Dent. Penguin is now the new mayor of Gotham City and Harvey swears to find his father's killers. A mysterious serum was accidentally released into Gotham City because of an explosion at Wayne Enterprises. Bruce encounters many meta humans and becomes friends with one named Clark Kent. Also, Lieutenant Gordon and his new partner Ellen Yin have to deal with the rising Maroni Crime Family and is William Dent really dead?
1. Three days after the death of William Dent, Harvey is now running Dent Tech and Penguin is the new mayor of Gotham City. Harvey learns of a project his father abandoned while working on it with Thomas Wayne. But a rouge military colonel kidnaps Harvey since he wants him to stop looking into that.
2. After watching his father's old Gray Ghost tapes, Bruce has a dream where Ava is a singer, Harvey is a bartender, Ethan and Lucius are detectives, other surprises and he is the Gray Ghost avenging William Dent's death. Meanwhile, a mysterious serum in the docks called the Big Boom is accidentally released into Gotham.
3. Bruce learns Ava is in a relationship with someone and gets shocked to discover that she's seeing the elderly Acting Principal Thompson. Bruce discovers that Thompson has the ability to hypnotize people into doing whatever he wants and Thompson uses Ava to steal objects for him to repay Luigi Maroni.
4. Alfred takes Bruce to a farm owned by Martha Kent to forget about William Dent, the Gray Ghost, and Acting Principal Thompson. Bruce meets Clark Kent and they both team up when Lex Luther is conducting a cloning project.
5. Under pressure from Penguin, Lieutenant Gordon and his new partner Ellen Yin investigates Balloon Man who is murdering corrupt Gotham officials. Meanwhile, Bruce returns to Gotham and tries to win Ava when a guy is hitting on her.
6. Harvey confronts a Big Boom infected boy who has psychic abilities to find out who killed his father. But a renegade scientist is after the boy.
7. After returning from Switzerland, Bruce, Tatsu, and Alfred are about ho head home until Alfred gets into a coma after being attacked by Death Stroke. Bruce seeks Harvey, Rhonda, and Lucius' help in using a device to go into Alfred's mind to find out who Death Stroke really is as Alfred fights to stay alive. Meanwhile, Gordon and Yin are forced to work undercover in Luigi Maroni's mob and are forced to immoral things.
8. Harvey is shocked to discover his father William is alive after killing Pino Maroni and that Luigi Maroni is holding William captive to revive a project that William and Thomas Wayne worked on. Gordon and Yin blow their cover in the mob thanks to corrupt Commissioner Peter Paulings (Toby Maguire) and Talia saves them.
9. Bruce, Ethan, Tatsu, and Lucius are forced to spend time in a school for mutants for a school summative project in order to graduate into grade 12. But Bruce, Ethan, and Lucius must save two superpower kids from their teachers. Meanwhile, William becomes the new mayor of Gotham forcing Penguin to work in the Iceburg Lounge and Harvey is wondering whether or not to go to New York City with Bethany.
10. Penguin wants Gordon and Yin to go after a deranged lunatic named Jack Napier after Napier destroys his night club. Bruce goes to visit Ava who is working as an intern in the hospital but gets taken hostage by Napier. It's up to Gordon and Yin to save them.
11. A low level thug uses signals against the city. Bruce needs Gordon, Rhonda, and Lucius' help to stop that thug. Meanwhile, William is angry when a television producer is making a show about his life but decides to seek his help since his popularity as mayor is slipping because of a gang war.
12. Gordon decides to make Selina Kyle stay in Wayne Manor since she saw who killed Bruce's parents before. Bruce and Selina go out on a picnic with Alfred by gets targeted by a Red Fists member. William tries to stop a mob war between Rupert Thorn and Tobias Whale since they're fighting over the Arkham Project.
13. Ava and Harry meets a girl who's deaf but can generate sound waves in the hospital. William tries to get the newly created Special Crimes Unit to capture the girl. Meanwhile, Penguin gets promoted to owner of the night club after exposing Fish Mooney's plan to overthrow Thorn.
14. Bruce tries to save Leslie from Matthew Thorn who kidnapped her to help save Rupert Thorn, who now needs surgery from the last episode.
15. Gordon and Yin goes after Birthday Boy and Axe, who are targeting people for Penguin. Bruce tries to protect William from Birthday Boy. But things gets worse when Birthday Boy kidnaps Barbara.
16. Continuing from the last episode Ethan discovers Penguin's involvement in the deaths of Thomas and Martha Wayne which puts him in grave danger.
-In episode 3, Harvey's Big Bad Harv personality activates and shoots Acting Principal Thompson and sends him into the river to die in order to protect Bruce and Ava. Lieutenant Gordon wanted to arrest Harvey, but he can't without Thompson's body. Bruce is shocked to learn that Ava is seeing Harry Prince.
- In a subsequent confrontation between Bruce and Penguin in Wayne Manor, Penguin reveals that his intention was for Weaver to murder the Waynes, but the couple ran into the mugger instead. Penguin then prepares to kill Bruce but is fatally shot by Alfred.
Bruce (smiling): What took you so long?
Alfred(looking down at Penguin's dead body): What a pity I just waxed the floor.
Axe is arrested and Birthday Boy is transferred to the Crane Institute for the Criminally Insane, run by Dr. Gerald Crane (the serial killer’s identity is revealed as Ray Salinger, an escapee from Crane's hospital).
-This season's main antagonist are;
Luigi Maroni ( Episodes 1-8)
William Dent, Penguin, Rupert Thorne (Episodes 9-16)
-Signal Man, Penguin, Rupert Thorne, Tobias Whale, the 100s, Talia Al Ghul and Joker are the only Batverse characters that appeared this season. The only non Batverse characters that appeared are Clark Kent, Martha Kent, and Lex Luther.