Plot

Harley Quinn gets in a fight with Killer Croc while trying to give him a cake as an apology for the Joker War. Croc does not except the apology and throws Harley out the sewer where she comes across some Gotham City citizens who blame her and all the "clowns" for what they did to Gotham. Instead of fighting them she tries reason with them, but they spit on her and she is forced to flee.

When she gets to her apartment, she finds the window open and an intruder inside, who turns out to be Batman. He scolds her for fighting Croc but she explains it is part of her mission to make amends to the other villains of Gotham. Batman agrees that he is letting Harley work with the Bat-Family as a form of penitence, and Harley is interested in when she gets her "Sweet Bat-Check or allowance or stipend, or at least her Bat Toaster" Like the rest of the Bat-Family.

Batman is about to scold her more when he gets a call from Oracle that there is a disturbance at Amusement Mile. Batman leaves and Harley follows, against Batman's wishes.

At Amusement Mile, citizens are attacking "clowns" and anyone who looks like they helped Joker during the Joker War. A young kid named Kevin is caught in the middle, because he burned a house during the war. Batman breaks up the mob and Kevin flees. Harley and Batman catch up to Kevin and Harley explains that Batman needs to take it easy on Kevin because, he had no idea what he was doing, and that only she can truly save him.

Batman agrees and leaves Kevin and Harley to get acquainted. Then later at Harley's apartment she finds that Batman has left her a Bat-Toaster.

Meanwhile in upstate at the Rockwood Hospital for the Criminally Insane, the "doctors" release Hugo Strange to fix the clown problem that Gotham is currently having.

A few days later, Mayor Nakano hires Hugo Strange to be the head of Gotham Secure and Fearless engagement program (SAFE) and Hugo's first order of business is to get all the clowns off the streets.

Meanwhile at a coffee shop Harley Quinn hears about the mayor giving Hugo a second chance and she losses it. She is then kicked out of the cafe where she runs into Kevin. Kevin explains he already got her, her morning coffee, and tries to explain that she shouldn't waste her time on him, because he can never be forgiven for what he did.

Right on que the pair pass a burnt down mall, and Kevin has a flashback to the night the other clowns convinced him to burn it down. As the gang flees Kevin hears a voice inside the building and waits until the police show up. His flashback ends and Harley convinces him he should go inside the shell of the mall with her.

Back at SAFE Headquarters, Hugo takes a pause from torturing the innocent people who he claims are Clowns, just because they have tattoos. Mr. Lockwood, one of Hugo's henchmen informs Hugo that Harley has been sighted in Gotham, to which Hugo sends some goons to collect her.

Back at the burnt-out mall, Kevin and Harley find random stuff and as they talk about how Kevin is still a good guy, they are ambushed by Hugo's goons. Harley can beat them up and take their van, not knowing there is a tracking device on the bottom of the van.

The Next day at SAFE Headquarters, Hugo Strange is testing a new formula on his latest patient, which kills the innocent man. Hugo then demands more of the formula and more test subjects. Upon leaving the lab Hugo tells his right hand man, Lockwood, that he is putting Lockwood in charge of collecting Harley Quinn.

Later that night, Harley and Kevin are having a support group for people who were forced to do bad "clown" things during Joker War. It doesn't look like anyone is going to show up but then a small group comes in. The group season seems to be going well, until Lockwood speaks up and upon being recognized releases his back up to capture Harley and her support group.

Harley fights back and Lockwood and his goons are forced to flee with their captives, which included Kevin. Harley tries to stop them, but she is forced to flee into the sewer where she comes across an angry Solomon Gundy.

In a very uncharacteristic moment, Harley Quinn and Solomon Grundy decide to play chess in the sewer while discussing how Harley is not a bad person. S.G. convinces Harley that she is good and she just needs to do things her way and stop trying to be like the Batman. Then Harley leaves to save her support group and her newest side kick, Kevin.

Meanwhile at SAFE headquarters, Hugo tells Kevin that he will fix the ex-Joker henchman, and if he can't Kevin will die trying. Hugo then injects Kevin with a new drug that causes Kevin to hallucinate.

Back on the streets of Gotham, Harley is making her way to SAFE headquarters to save Kevin. She uses a stolen Bat grappling hook to make it inside and fights guards all the way up the tenth floor where she is ambushed by Hugo and two of his goons.

Harley and Hugo then have a calm conversation about why Hugo has a obsession with the Batman. This calm conversation turns into a shouting match when Harley pushes Hugo's buttons. Harley then uses a bathroom break to call Solomon Grundy who comes to SAFE Headquarters and helps Harley rescue Kevin and the other support group members who were kidnapped by Hugo and his goons.

After Harley makes an escape Hugo has a meeting with his mysterious employer, Keepsake.

Sometime later, Harley is running through the streets of Alleytown, trying to escape the Magistrate. Things look bad when she ends up in a dead-end, but luckily Catwoman comes to her aid. After sending the Magistrate goons running Catwoman demands to know why Harley is in her part of Gotham, to which Harley replies with her usual rabbling recap of recent events, ending in in the fact that she is looking for Hugo Strange's drug lab. Catwoman agrees to help Harley, under the condition she never comes back to Alleytown.

Back at SAFE headquarters Hugo meets with Scarecrow to join forces to take control of Gotham. Scarecrow refuses, and after beating up Keepsake for stealing his fear toxin, leaves Hugo with a threat to stay out of his way.

Elsewhere in Alleytown, Harley and Catwoman find Hugo's drug lab and are able to stop production, but Lockwood makes an escape with a van full of toxic poison. Catwoman almost has him, but he throws poison at her, and Harley sacrifices herself to save Catwoman, taking a vail of poison to the face.

Later, back at Selina's apartment, Harley wakes up from the effects of the poison. Selina thanks her and the two have a moment before Catwoman swings out over Gotham attempting to be a hero again.