After responding to a break-in at the chemical labs at Stagg Industries, Batman rescues a security guard named Rex Mason who had been exposed to a weaponized toxic gas known as "Project Metamorpho." Soon, Rex begins to mutate and gains the ability to manipulate the elements of his own body. Terrified and unable to control his new abilities, Rex becomes a fugitive. Realizing that this metamorphosis is slowly killing Rex, Batman sets out to find a cure. But Rex is only concerned about one thing: Sapphire Stagg (the woman he loves) and he would risk all of Gotham to be with her. But her father Simon Stagg holds secrets of his own and will do anything to keep them apart.

Tobias Whale is the most powerful gangster in Gotham City, and, after years of trying, Lt. Gordon finally has the evidence to put him away for good. But Whale is not going to be "harpooned" easily. After his lawyer demands that Gordon release Whale, Gordon's daughter Barbara is kidnapped. With no other options and time running out, Gordon is forced to ask Batman for help. While monitoring Whale's men, Batman learns that Barbara has been taken to "The Cauldron" (a former industrial park that became the most dangerous part of the city following the financial crisis years ago) which is populated by a gang of criminals known as "the Ghosts." With Katana's help, Batman stages a raid on the Cauldron. But the real threat here is not the Ghosts, but the man guarding Barbara: Whale's chief enforcer, Phosphorus Rex!