Bruce Wayne met with Lucius Fox to discuss the status and business options of a crumbling Wayne Enterprises. After their discussion, Lucius was curious as to why Bruce did not inquire about any new equipment (for his Batman activities) and noted that their meetings used to "end with an unusual request." Bruce then replied that he was retired from Batman, but Lucius coerced him to look at some new stuff anyway: "just for old time's sake." They soon entered the Applied Sciences Division which was still kept secret by Lucius and Fox then unveiled a new vehicle.
Bruce then asked Lucius what the vehicle was called to which Fox replied: "it has some long, uninteresting Wayne Enterprises designation", but he simply chose to dub it "The Bat". Fox also noted that it did indeed "come in black," (a reference to the first film). While mentioning many of its features to Bruce, Lucius noted that he did not design a functioning auto-pilot, but that someone of Bruce's intellectual caliber would be able to design one.
Later on, when Bane attacked Gotham City's Stock Exchange, Bruce returned to Gotham as Batman and chased Bane and his henchmen on the Batpod. After Batman managed to stop one of Bane's Henchmen and recovered a piece of technology, he was pursued by the GCPD, who then attempted to apprehend him (as Batman was still wanted for the crimes that Harvey Dent had committed in The Dark Knight) rather than capture the true antagonists. Batman escaped into a dark alley where the police cornered him, but escaped by flying out of the alley in the Bat. Batman then ran into Selina Kyle and helped her escape Bane's Henchmen.
After Bruce escaped The Pit and returned to Gotham, he convinced Selina to help him get Lucius out of captivity so that he may get him access to his Batman equipment, including the Bat, which Bruce secretly parked on top of Wayne Enterprises.
When the GCPD returned to Gotham from being trapped underground for months, they confronted the escaped Blackgate Prison Prisoners along with Bane's Mercenaries who were armed and had access to Tumblers. As one of the Tumblers took aim at the cops, Batman arrived in the Bat and disarmed it by firing on it. After Selina rescued him from Bane, Batman took off in the Bat and followed Talia al Ghul, in order to recover the fusion reactor core, which was converted into a Nuclear Bomb.
After Batman forced the truck that held the core to crash underground, Talia revealed that she found a way to keep the bomb on track to exploding. Batman then attached the bomb to the Bat via a cable and flew out to the ocean in order to protect Gotham from the blast. After Gotham honored Batman as a hero and Bruce was privately mourned, Lucius discovered that Bruce had designed an auto-pilot on the original Bat when he logged in six months ago (when Lucius first told him about the vehicle), which hinted that Bruce had survived the blast.