A robber escapes a bank at night. As the alarms go off, he tosses his loot in the car and a voice calls to him from the darkness, advising him to surrender. Batman slips through the shadows and finally approaches him when he wastes his shots. The robber considers whether to go for his backup piece, but when he draws it Batman easily disarms him. However, the robber's partner attacks Batman, using a pair of metal-enhanced fists. The other robber grabs his gun and fires, and Batman disarms him with two Batarangs before disposing of his partner.
Elsewhere in Gotham, billionaire Simon Stagg runs down the street, yelling for help. Two villains, Professor Pyg and Mr. Toad, pull up in their roadster and open fire on Stagg. He runs into the nearby building and Toad blows open the doors so that they can drive in. When Stagg warns them how powerful he is, they shoot him with a drugged dart and say that they're hunting him because of what they've done to their kind--animal kind. Toad then clubs him unconscious.
The next morning, Bruce Wayne is sleeping in late when a masked figure enters his bedroom and attacks him. Bruce fights back and finally subdues his opponent... his butler, Alfred, testing him once again. Alfred complains about Bruce's slow performance, but Bruce doesn't want to hear it. The butler reminds him that his job is to protect him, and Bruce reminds him that his job is to protect Bruce Wayne, not Batman.
At breakfast, Bruce considers an invitation to the ARGUS club and tells Alfred that he can't go out into the field at his age. As they talk, Bruce notices a newspaper article about Stagg's abduction. They turn on the news, which is broadcasting a video from the abductors. Pyg and Toad show off a plaque with Stagg mounted on the wall, and recite a nursery rhyme promising that he's not the last one they will hunt down.
Batman and Alfred go to the Batcave and try to check Stagg's financials, figuring that the key to his abduction lies in the nursery rhyme, based on a real-life case of crooked land dealing. However, Staff's files are encrypted and they can't tap them. Batman then reviews the ransom video and, magnifying it, spots a plaque with the name "Michael Holt" on it. Holt is another Gotham billionaire industrialist and Batman heads off to protect him while Alfred works on decrypting the files. Once Batman leaves, Alfred calls someone and says that they need to meet.
Pyg and Toad are driving after Holt as he tries to get away through the traffic. Batman pulls up and snags the roadster with a cable, but Pyg cuts it free and Toad fires a bomb at Holt's car. Before it can hit, Batman pulls up and intercepts the bomb, but the explosion knocks both cars off the road. The villains discover that Batman has escaped and drive off with Holt, while Batman collapses in a nearby alley from his wounds.
At Wayne Manor, Alfred meets with Tatsu Yamashiro, who provides him with the information he needs from Stagg. When she says that she'll be in town for the night, Alfred asks if she's considered his offer. She says that the answer is still no and Alfred says "Please," and Tatsu drives off. Alfred calls Bruce on his cell phone, and Batman manages to turn on the phone. As he explains what happened, Alfred says that he uploaded Stagg's information to the server. Pyg and Toad arrive and knock out Alfred, mistaking him for Bruce. They see the phone and, going by the caller ID, tell Bruce that they'll be meeting soon enough.
When Batman returns to the Batcave, he downloads Stagg's files and discovers that he and Holt were involved in a land deal where they purchased a wetlands and animal preserve when oil was found there. Batman is surprised to discover that he was the third investor.
At the oil refinery in the wetlands, Stagg and Holt beg to be released. Pyg informs them that they are going to hunt the three of them, just like they hunt and drove off the animals occupying the wetlands. The villains release them and give them a five-minute head start, and the three men run off.
As Batman drives up to the refinery in the Batmobile, a computer scan informs him that the building is unstable and there are methane pockets scattered throughout the area.
The three men, chained together, make their way through the refinery. Alfred spots a wire and realizes that it's attached to a booby trap. He tells them that it's time to fight rather than run and hands Stagg a pipe.
Batman makes his way into the refinery and knocks loose a piece of metal. The sparks set off a methane pocket.
Stagg makes his way over the wire and continues on with the others. Toad tosses a bomb at them and they run back, and Stagg sets off the trap. Alfred shoves him out of the way just in time, but is knocked out in the process. Above, the stairwell Batman is on collapses from the explosion and he quickly escapes on a Batline.
Alfred's chain is broken and his ankle is broken. Holt refuses to abandon him and before they can do anything else, Pyg and Toad attack them. Alfred tells Holt and Stagg to run but Toad knocks them out with a sonic blast, and a cage trap drops on them. As Toad attacks Alfred, Batman arrives and knocks him back. He attaches a small explosive to Toad, stunning both villains. He gives Alfred a painkiller and a taser and then goes after the villains, while Alfred gets the two men out.
Pyg and Toad recover and Toad blasts Batman with a sonic blast while Pyg attacks with his surgeon's saw. Batman manages to disarm him but Toad throws a bag full of bombs and the villains run off. The vigilante runs just ahead of the blast and gets out as the refinery goes up in flames. Stagg is furious that Batman endangered them, but Batman ignores him and tells Alfred that the villains have escaped... for now.
The next day, Lt. Gordon is giving a statement on TV while Alfred recovers from his injury. Batman tells his friend that Keystone Park has been given back and admits that he didn't know his company purchased it. He admits that he went in blind and that he needs Alfred to protect him in both of his identities. Alfred reminds Bruce that he promised his parents that he would watch over him, but it will take months for his ankle to heal. Since there will be a time when he can't be there, he's hired Tatsu to serve as Bruce's driver and bodyguard.