A psychiatrist, Doctor Hurt was involved in a program which created three "replacement Batmen" with the participation of the GCPD Sometime after the three replacements had been trained, Simon Doctor Hurt was hired by the Pentagon to oversee an isolation experiment. During this process, he gave Batman a post-hypnotic trigger connected to the phrase "Zur-En-Arrh". He also arranged for the replacements to fight the dazed Batman, but they were defeated. Batman suspected nothing of this.
Going over his notes on Batman's psychology, he realized that Batman was "powered by tragedy" and set about traumatizing the three replacements, ostensibly to make them better crime-fighters.
Many years later, Doctor Hurt was working with the Black Glove when they decided to target Batman and his allies. Their first attack consisted of character assassination on the Wayne family, by spreading information to suggest that Batman's father somehow survived his murder by Joe Chill (to the point that he had arranged for the 'attack' himself in order to conceal his own debauchery). Doctor Hurt then, using the Zur-En-Arrh trigger in conjunction with drugs, sent a dazed and confused Bruce Wayne onto the streets of Gotham City with no memory of his life. Furthering this attack, he claimed to Alfred Pennyworth that he was actually Thomas Wayne himself, although Alfred denied this claim had any weight in reality.
However, Batman survived thanks to years of preparation, culminating in him confronting Doctor Hurt on the roof of Arkham Asylum. He accused Doctor Hurt of being Mangrove Pierce, an actor, acquaintance and occasional impersonator of Thomas Wayne, but Hurt claimed that he had actually "skinned Mangrove Pierce alive and wore him to Mayhew's party", which likely refers to the events of the "Club of Heroes" arc.
Doctor Hurt was believed to be dead after a helicopter explosion, but somehow survived and reappeared approximately six months later in Mexico, disguised as the drug lord El Penitente, but left to return to Gotham City. With the Joker working as an unreliable ally, Doctor Hurt used the Circus of Crime to release a drug into Gotham City's air with the intention of driving the city mad, subsequently making a public return as Thomas Wayne with the intention of setting up his headquarters in the Batcave. Doctor Hurt shot Dick Grayson in the back of the head and attempted to force Damian Wayne to swear allegiance to him in order to save Grayson's life. However, Grayson and Damian had already anticipated his attack, Grayson surviving Doctor Hurt's attack relatively unharmed while Doctor Hurt's attempts to open the box that Bruce Wayne left in the past revealing nothing but a Batarang and a note saying "Gotcha!", the room subsequently filling with smoke as another Batman appears, marking Bruce Wayne's return to the fold. In the subsequent confrontation, Doctor Hurt attempts — and fails — to trap Bruce Wayne in a prison in the Batcave, but nevertheless escapes through the cave's water access while Bruce is busy rescuing Alfred. Having escaped to a graveyard, Hurt is confronted and defeated by the Joker. The Joker doses Doctor Hurt with Joker venom and buries him alive, claiming that he proved to be a disappointment as a "new" archenemy. The Joker claims that he has "taken care" of Doctor Hurt, but Bruce Wayne is not quite willing to believe that the Doctor is truly dead.
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