7. Ace Chemicals

Complete story — includes the ending

On the anniversary of the Wayne murders, Jeremiah uses two surgical doppelgangers of Thomas and Martha Wayne to force Bruce to relive his parents' deaths, hoping to become "connected" to him. Bruce and Alfred escape as Jeremiah blows up Wayne Manor, and Selina abandons Cobblepot to assist Bruce. Gordon and Lee discover Jeremiah is developing a toxin at Ace Chemicals, and are hypnotized by the Mad Hatter. Jeremiah kills the doppelganger couple and attempts to execute Gordon and Lee at Crime Alley, but Bruce and Selina rescue them. Jeremiah activates the toxin, forcing Gordon to drive it into the Gotham River; due to the water pollution, the government decides against mainland reunification. After a showdown with Bruce at Ace Chemicals, Jeremiah falls into a chemical vat and is left disfigured and brain-dead. Barbara, for the sake of her unborn child, forms a truce with Cobblepot and Nygma, who plan to escape Gotham on a self-built submarine.