Once Thorne was arrested for his crimes, Bruce had to deal with Catwoman, who had returned to Gotham and became jealous of his relationship with Vicki Vale.  Batman was forced to confront Catwoman and made her understand that their relationship was over.  In the midst of this love triangle, Bruce was attacked by Hugo Strange, who had faked his death and returned to claim the mantle of Batman and kill Bruce Wayne to adopt his identity as well. 
After dealing with various criminals including Solomon Grundy  and the Squid  Bruce was introduced to the Todd Family.  Right after this, Batman came in conflict with a new criminal in town called Killer Croc, who wanted to become the new crimelord of Gotham.   Croc created a path of destruction and murdered Joe and Trina Todd, leaving their only son, Jason, an orphan. After Batman took Croc down, he decided to look after the kid, much like he did with Dick Grayson. 
A month later, Jason started training to become Batman’s partner, a goal not shared by Bruce.  When Man-Bat returned to challenge Batman, Jason was kidnapped by the monster  and combining their forces, Batman and Jason defeated the monster, turning him back to normal. 
Despite his obvious enthusiasm to become Batman’s partner, Jason was denied the chance and he ran away from Wayne Manor, Batman followed him to the circus, where he captured a criminal called Chimera  with help from Jason. This made Batman reconsider the decision of giving Jason a chance to become his partner.  Upon their return to Gotham, Batman had to save Vicki Vale from the Joker and he travelled to Guatemala, where he stopped Joker’s plans of taking over the country.   However, Batman was only able to defeat Joker with help from Jason Todd, who had taken Dick Grayson’s outfit and dyed his hair black to become the next Robin.  At first, Batman opposed the idea, but when Jason helped him take down Poison Ivy, Batman finally agreed to let Jason become his new partner.  After this, Dick Grayson appeared in the Batcave and informed Batman and Jason about his decision of leaving the identity of Robin in the past. However, since he was aware of Jason’s new partnership with Batman, he allowed the young one to become the new Robin and continue his legacy. 
With Jason as his new partner, Batman and Robin stopped various criminals including Crazy Quilt,  Doctor Fang,  Catman,  Scarecrow,   Mister Freeze  and many others. Unfortunately, the legal paperwork to acquire Jason’s guardianship was overlooked and Bruce lost the kid to the child welfare bureau. 
After dealing with the Riddler once more,  Batman confronted the Thief of Night, but couldn’t stop him in their first encounters.  Eventually, Batman learned that the Thief of Night was working with an employee of Wayne Enterprises called Natalia Knight. She had suffered an accident while working on the Gotham Observatory for Wayne Enterprises, which caused her skin to become white. When Bruce met her in person, he was immediately fascinated by her and used her connection to finally capture the Thief of Night.  Shortly after the Thief’s trial, Batman captured Nocturna while she tried to release her adoptive brother. 
A short while later, Batman confronted a group of thieves called More Help Nightmares, Inc., led by one Nightshade,  unaware that they were all led by Nocturna. Having stopped Nightshade, Batman learned that Nocturna had filed the adoption papers of Jason Todd in an attempt to force Bruce Wayne to marry her and enjoy a life of luxury with his fortune.  As soon as this happened, Nocturna’s associate, the Thief of Night escaped from prison and became the Night-Slayer. While chasing down the criminal, Batman came across Nocturna, who turned against the Night-Slayer and helped Batman, before realizing they were both attracted to each other.