| Synopsis
| - Stephanie Brown is enrolled in the Saint Hadrian's Finishing School for Girls, which is supposedly a training ground for assassins. After she is introduced to the group, Stephanie meets a group of girls, who suddenly pull out guns at her. She easily disarms one of the girls, but a teacher comes in and takes Stephanie down, sending her to detention.
As Stephanie sits outside the Headmistress's office, she befriends another student, Jolisa Windsor. Miss Hexley and the Headmistress study Stephanie's archive, discovering that she is Cluemaster's daughter.
Stephanie continues her studies at daytime, while she investigates the school as Batgirl at night.
Eventually, Stephanie and Jolisa become so experienced that the Headmistress invites them to the Tower, a place where the best students go. At the Tower, students tie ropes around Stephanie and Jolisa's necks and feed them with special wafers that make them loyal to Leviathan. This s part of an initiation ceremony, which is led by the Son of Pyg, Professor Pyg's son and a Leviathan officer.
Son of Pyg begins interrogating the two girls, saying that one of them betrayed the school. When he threatens Jolisa, Stephanie frees herself and saves Jolisa. As they escape the Tower, Son of Pyg and the Leviathan girls chase after them. Reaching the rooftop, Stephanie changes into her Batgirl outfit and takes Jolisa to the courtyard.
Instead of escaping, Batgirl locks the school's gates so that no one gets out. Just when the students prepare to fight, the school's gardener reveals himself as Batman, who takes Son of Pyg down. The teachers refuse to help the students, saying that they are freelance and the students are on their own. While Batgirl fights the girls, Jolisa pulls out a gun on her. Batgirl realizes Jolisa ate the mind control wafer, so she has to defeat her.
Batman reaches the Headmistress's office, and finds Miss Hexley who aims her crossbow at him. Batman reveals that he knows all of the school's secrets and operations, including the school's allegiance to Leviathan. As Hexley shoots him, Batgirl breaks through the office's window and takes her down, while Batman catches the arrow at mid-flight.
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Later, at WayneTech, Bruce and Lucius Fox examinate the crystal Batman confiscated from Doctor Sivana. Lucius explains that the crystal can interact with light and other forms of energy unknown to nature. Lucius also shows Bruce the new army of Bat-Robots for Batman Incorporated.
Batman, Dick, Tim and Damian infiltrate Doctor Dedalus's ship, fighting several enemies through his maze. Batman passes through one of the maze's door and finds Dedalus and a large screen with the voice of Leviathan's Headmistress. Dedalus poisons Batman with a toxin designed by Professor Pyg. Dedalus taunts Batman, saying that in every Batman Incorporated agent dies every five minutes.
Meanwhile in a mansion at Mtamba, Desmond Zavimbi is being interviewed by an African inspector, who believes Desmond to be Batwing. Suddenly, Batwing and his allies barge into the mansion and release smoke, kidnapping Desmond. However, Batwing takes his costume off, revealing himself to be Desmond, while David pretended to be Desmond so that he could investigate Leviathan's activities. As David puts his Batwing costume on, he talks with Oracle, saying that he has something important to tell everyone about Leviathan.
At Dedalus's ship, Batman discovers that Dedalus is in fact a decoy, while the real Dedalus is in another part of the maze.
In England, the Hood obtains information on Leviathan, but before he can tell Oracle what he found, an unknown assailant shoots him.
Dick, Tim and Damian defeat all of Dedalus's henchmen, but when they unmask them, they discover they are all in fact brainwashed Batman Incorporated agents. They also realize that the maze is a giant mechanism equipped with rotating drums and identical rooms. Damian enters one of the rooms, trying to find his father.
Batman reaches the last room and finds a corpse dressed in Dedalus's costume. Then, he is attacked by Gaucho, the last brainwashed agent. The real Dedalus appears and activates a detonator, setting off explosions in the ship's stern.
Meanwhile in space, the Outsiders infiltrate Leviathan's orbital HQ. The Outsiders then find Lord Death Man, and then the station explodes.
Oracle activates the Ro-Bats and reaches the Leviathan ship.
Dedalus and Gaucho take Batman to the center of the labyrinth, and Dedalus says that he has placed bombs across the world. Gauncho reveals he gave Batman the antidote to the toxin and tries to attack Dedalus, but Dedalus stabs him in the neck with a blade. He then begins torturing Batman with electricity while Batman tires to reach the failsafe that will deactivate the bombs. When Dedalus is about to kill Batman, Robin reaches the center of the labyrinth and kills Dedalus instead. Batman manages to deactivate the bombs, ending the crisis.
As the Ro-Bats take the ship to a nearby shore, Batman, Dick, Tim and Damian discover a hidden room that contains the head of Jezebel Jet. She was never the leader of Leviathan. A nearby phone rings and Batman answers, revealing the true leader of Leviathan: Talia al Ghul. Having Leviathan and the country of Mtamba under her control, Talia declares open war on Batman.
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