At Stagg Industries, security guard Rex Mason is with his girlfriend Sapphire Stagg, the daughter's boss. She doesn't care who knows about them together, but Rex is worried that her father will find out. An alarm goes off and Rex goes to investigate.
Batman is driving down the streets of Gotham when he gets word of the alarm at Stagg Industries. He has the computer plot a route there.
Rex enters the computer room and sees an intruder. The thief runs off into the Project Metamorpho section and enters a chamber. He runs out one side as Rex runs in, and the chamber closes, sealing the security guard in. The intruder activates the controls and chemical gasses fill the chamber, and then flees. Batman arrives and vents the chamber, and then runs in and gives Rex oxygen from a respirator.
Later, Bruce and Alfred stop off to buy hormone-free bovine glands. They discuss the break-in and Stagg's reputation for off-the-book experiments, and wonder how someone got in past the high-tech security. Tatsu is away monitoring Jason Burr after the recent abduction attempt. Dr. Bethany Ravenclaw is coming out and greets Bruce, and soon talks Bruce into taking her to a fundraising dinner. She leaves and Alfred notes that he's flustered.
When Rex wakes up, he finds Sapphire and Simon at his side. Sapphire is holding Rex's hand, and Simon assures Rex that he supports his daughter's decision. Rex promises to always keep her safe and then goes into the next room, feeling nauseous. Simon warns his daughter that Rex was exposed to gasses that have never been tested on humans, and worries that there could be complications.
In the neighboring bathroom, Rex reaches for a towel and discovers that his hands have transformed. He winces in pain as the transformation spreads up his arms, and then screams in pain. When Sapphire goes to the door, Rex smashes it open, revealing that he has mutated into a gigantic beast made up of dozens of different chemical components. They don't recognize him at first, but Rex moans out Sapphire's name. She goes to him, but a security guard comes in and opens fire. Rex is immune to the bullets and leaps out the window.
As Alfred drives him home, Bruce tries to review the security footage from Stagg Industries, only to discover that Stagg has it secured behind a firewall. Alfred is forced to swerve as a car drops into the street ahead of them. As Alfred pulls over, the police arrive as the transformed Rex goes on a rampage. Bruce dons his costume and tries to secure the rampaging creature. Rex throws him aside and then transforms his body into phosphorous, burning through the line. The transformed security guard runs off and Batman follows, pinning his hands to girders. This time Rex transforms his hands into super-strong metal, pulling the girders free. Batman gets out just in time as the building collapses, Rex smashes through the rubble, unharmed, and Batman recognizes his face. The transformed security guard runs into an alley and Batman tells him to stop. Rex gasps out that he doesn't want to hurt anyone, and tells Batman that he doesn't want to harm Sapphire. He then transforms into liquid and flows into the sewers.
Batman takes a sample of the remaining liquid and analyzes it at the Batcave. He informs Alfred that Rex was exposed to gasses that have destabilized his molecular structure. The process will soon prove fatal unless he can find him and administer a cure. Batman then breaks into Stagg Industries and hacks the computers on site. As he works, Bethany calls to remind him that they have the fundraiser in a half-hour. Batman spots the intruder on the footage and hangs up, and confirms that someone erased all of the files on Project Metamorpho. The only one with that level of access is Simon, and Batman hacks his personal computer. Simon had Rex and Sapphire under constant surveillance.
Simon arrives in the computer room and opens fire on Batman. Batman takes cover and warns Simon that he's going to jail for setting up Rex for the accident after he discovered Sapphire was with a man below his station. The industrialist boasts that Project Metamorpho is a technique for weaponizing genetic tissue, creating the perfect soldier. A "Metamorpho" is not only immune to elements, but can manipulate them against the enemy. When Batman points out that it will kill Rex, Simon dismisses it as incidental damage. His security guards arrive and fire at Batman, who blasts open the ventilation shaft and leaps out into the night to make his escape.
Sapphire is at home sleeping, but wakes up when she realizes that Rex is in her room. She insists that he turns on the light, and Rex explains that he isn't under control of his form because it responds to his emotions. When Sapphire wonders why it happened, Batman arrives and tells them that Simon is responsible. She doesn't believe it, but Rex realizes the truth. Batman warns that every time he changes, his body becomes increasingly unstable. Furious, Rex attacks Batman, who drives two tasers into his back. Sapphire goes to him and is shocked when he touches her, and Rex incorporates the tasers into his body and then blasts Batman with them. "Metamorpho" picks up the unconscious Sapphire and runs off into the night.
Batman wakes up when he gets another call from Bethany. He apologizes for cutting her off earlier, and offers to make it up to her for standing her up... later.
Metamorpho flees into the sewers with the unconscious Sapphire. He heats up his hands and then draws Simon's name in the concrete.
Simon returns to his office and finds Batman waiting for him. Batman warns him that Rex knows Simon is responsible for his condition, and that he told him to lure him there. The vigilante tells Simon to give him access to Project Metamorpho so that he can find a cure.
Metamorpho, carrying Sapphire, walks up to Stagg industries. The security guards open fire but Metamorpho creates a shield, knocks out the guards, and flies into the building. Meanwhile, Batman is in the transformation chamber, trying to work out a way to reverse Metamorpho's condition. He tells Simon that he needs more time and orders him to stall Metamorpho. The industrialist runs back to his office to get a weapon just as Metamorpho bursts in. Simon insists that he only wanted what was best for Sapphire and opens fire.
Batman finishes his adjustments and tells Simon to lure Metamorpho to the lab. The industrialist lures him to the lab and into the transformation chamber, and Batman snags Sapphire and pulls her clear. They seal the chamber doors and Simon initiates the procedure. They flood the chamber with gas, but Metamorpho remains in his transformed condition. Sapphire goes to the window and Metamorpho asks if she can still look at him and feel the same. She reluctantly admits that she can't and Metamorpho smashes open the exhaust vent. He then lets himself to transform into gas and be dispersed into nothingness.
Furious, Sapphire runs to her father, blaming Batman. Simon accuses Batman of murdering Rex, but Batman reveals that he downloaded the files revealing Simon's involvement. The police have them, and Batman advises Simon to get his legal affairs in order. Sobbing, Sapphire runs away from her father.
Later, Bruce meets with Bethany for dinner. She wonders what he was doing that was so important he had to break their first date, and Bruce said he had to help someone with relationship problems. Bruce admits that he wasn't able to help and that personal relationships aren't his strong suit. As Bethany says that she'll try to change that, Alfred calls and Bruce says that he has to take it. As he walks off, Bethany sends a message to someone saying that Bruce is hooked.
In the sewers, Metamorpho slowly reforms.