| ShortSummary | - With the League of Assassins knowing where the Soultaker Sword is, but unable to get Katana to return it, Silver Monkey decides that the only course of action is to kidnap Bruce Wayne and hold him for ransom at the A.R.G.U.S. Club... his life for the sword. When Katana shows up to turn over the Soultaker Sword and rescue Wayne, Alfred causes a diversion buying Wayne enough time to suit up and join the battle. Teaming up with Katana to fight Silver Monkey and men, Batman finds himself in an all-out ninja fight when Lady Shiva shows up in person.
- At a rally to announce Harvey Dent's run for mayor, Bruce Wayne is "assassinated" by Batman. Bruce survives, but instead of telling the world, Bruce decides it's better to stay dead while Batman hunts for his imposter.
- Batman and Katana encounter a strange Man-Bat creature, an experimental result of Professor Pyg and Mister Toad's animal army of mutant humans, and so Toad can get a wife. Meanwhile, in order to keep his enemies closer, Bruce Wayne befriends Harvey Dent and the captain of the SCU, Dane Lisslow, with whom he makes a strong connection.
Note: Barbara Gordon takes the codename "Oracle" after she helps Katana.
- When Batman and Katana are ambushed by Killer Croc in the subway, it's up to Barbara Gordon to save them. There's only one problem: Barbara is on a date.
- Professor Pyg and Mister Toad are back, and this time, they've set their sights on Gotham's elite couture culture. Leaving clues that only Batman can decipher, they attack both a fashion model and a clothing designer. Even though Batman and Katana are able to save them, they end up uncovering Professor Pyg and Mister Toad's master plan: to destroy the yacht where the after-party for Gotham's Fashion Week is being held.
- Batman, Katana, Commissioner Gordon, Mayor Grange, and Tobias Whale all wake up after being drugged and kidnapped by Humpty Dumpty. According to Dumpler, there is a culprit among them and the only way to escape his Murder Mystery Game is to figure out who. With each clue, however, the game becomes deadlier and begins to take its toll on Batman who's obsessed with solving the mystery and defeating Dumpty.
- Introducing the prototype of his newest product to the entire world, the Ion Cortex, a powerful device capable of solving the world's energy crisis, Bruce Wayne hires brilliant scientist Dr. Jason Burr to work on the project. The announcement also draws the attention of the League of Assassins. While Batman is in Gotham investigating the League of Assassins, the League's agent Silver Monkey is sent to kidnap Dr. Burr. When Silver Monkey attacks Wayne Manor, it is up to Alfred and Katana to keep the assassin at bay until Batman arrives. But Katana is armed and ready for the task with the legendary Soultaker Sword, a sacred weapon she stole from the League of Assassins back when she used to work for them.
Note: This episodes marks the first time where Tatsu Yamashiro is referred to as "Katana".
- A new villain has arrived in Gotham to challenge Batman: Anarky. Resembling a ghost image of Batman, Anarky prides himself on his brilliance and intends to prove it to Batman by manipulating a pair of street thugs, Junkyard Dog and Daedalus , to do his bidding. But Anarky's real plan is far more devastating: seeking to create a disaster seen by all of Gotham and proving once and for all that even the great Batman is powerless to protect his fair city from the clutches of Anarky.
Note: This marks the first appearance of Anarky, Batman's arch nemesis in the series.
- As Batman and Katana fight their way through the GCPD and the SCU, Deathstroke makes his escape in the Batmobile. By the time Batman and Katana have eluded the police, their worst fears have been realized: Deathstroke has found the Batcave and taken Alfred hostage. And if Batman ever wants to see Alfred alive again, he must come to the mansion... alone. Meanwhile, Harvey Dent reveals his true nature as Two-Face, and breaks off his partnership with Anarky.
Note: At the end, it is implied that, Batman, Katana, Oracle, Man-Bat, and Metamorpho form the Outsiders.
- After stealing a valuable package from the League of Assassins, Anarky pins the blame on Batman. At the same time, he informs Batman where he can find Lady Shiva: the Gotham Contagion Research Center . Although they know it's a trap, Batman and Katana go anyway. Unfortunately, the assassins accidentally release an airborne mutative toxin into the building called Calibosix. Now Batman, Katana, and Lady Shiva have to escape the building before its breach protocol is initiated, while staying ahead of two mutated assassins. In the end, Anarky gives Lady Shiva back the package he stole which contains the body of Ra's al Ghul.
- Tobias Whale is the most powerful gangster in Gotham City, and, after years of trying, Lt. Gordon finally has the evidence to put him away for good. But Whale is not going to be "harpooned" easily. After his lawyer demands that Gordon release Whale, Gordon's daughter Barbara is kidnapped. With no other options and time running out, Gordon is forced to ask Batman for help. While monitoring Whale's men, Batman learns that Barbara has been taken to "The Cauldron" which is populated by a gang of criminals known as "the Ghosts." With Katana's help, Batman stages a raid on the Cauldron. But the real threat here is not the Ghosts, but the man guarding Barbara: Whale's chief enforcer, Phosphorus Rex!
- Batman makes an unlikely alliance with Silver Monkey to escape from the League of Assassins. Meanwhile, Katana, Alfred, Lieutenant Gordon, and Barbara take action as Ra's al Ghul's attempts to cleanse the city during the blackout has left it terrorized by the Ghosts and other criminals.
- A master thief known as The Key, has stolen the most valuable piece of code-breaking software in the world. But when he is sent to Blackgate, Batman has himself arrested and sent to prison to recover the dangerous software. Unfortunately, the Key has been taken by the prison's "king", Killer Croc. Batman must now fight his way through Blackgate's entire prisoner population while Katana works with Oracle to save him.
Note: Penguin is referenced by Harvey Dent and is seen on a wanted poster.
- Batman is hot on the heels of an extremely dangerous thief named Magpie, who not only sports razor sharp fingernails laced with poison but is also invulnerable to pain. But Batman is not the only one after her. Lieutenant James Gordon is after her as well. And the two will ultimately go head-to-head to catch her.
Introducing Characters: Magpie / Margaret Sorrow, Oracle / Barbara Gordon, Bethanie Ravencroft, Thomas Wayne, Martha Wayne, Lunkhead, and Joe Braxton
Trivia: Lunkhead makes a cameo appearance in this episode, but not as a villain.
- Ava Kirk, an old friend of Bruce Wayne's comes to him for help, when her father, Paul, has been cloned by The Council, a mysterious organization to create an army of super soldier Manhunters.
- Desperate to gain access to the Ion Cortex after the failed kidnapping of Jason Burr, Lady Shiva sends one of her specialized agents to steal the information directly from Burr's mind: the wall-crawling, half-computer assassin Cypher. Batman and Katana try to stop Cypher, but Katana gets herself captured. Now, Batman must find a way to take down Cypher while he is in control of both Burr and Katana.
- Batman continues to work in secret while the world continues to believe that Bruce Wayne is dead. Meanwhile, as Harvey Dent recovers in Gotham Hospital, he decides to take matters into his own hands. Blaming Batman for destroying his chances to become mayor, he enacts martial law in Gotham, instructing the police to hunt down Batman and bring him to justice... dead or dead.
- Desperate to rid the city of Batman, Harvey Dent allies himself with Anarky, who recruits a new "hero" to take Batman's place: the newest member of the Special Crimes Unit, Deathstroke.
- Batman and Katana team up with Rex Mason as they combat an army of armored thugs that have been terrorizing several parts of Old Gotham after they were supplied the high-tech armors from Stagg Enterprises. In addition, they also dodge Harvey Dent's newly-created Special Crimes Unit, which has been ordered to take down both the armored criminals and the vigilantes fighting them.
Note: At the end of the episode, Rex ends up taking the codename "Metamorpho" and alludes to the future emergence of the Outsiders.
- Unbeknownst to both Alfred and Katana, Batman has been making visits to Blackgate Penitentiary to see Magpie. Helping her to regain some of her former memories, Batman has felt guilty that she did not get the psychological care she needed. When Magpie sees Batman with Katana, however, she breaks out, willing to kill Katana in a jealous rage.
- After responding to a break-in at the chemical labs at Stagg Industries, Batman rescues a security guard named Rex Mason who had been exposed to a weaponized toxic gas known as "Project Metamorpho." Soon, Rex begins to mutate and gains the ability to manipulate the elements of his own body. Terrified and unable to control his new abilities, Rex becomes a fugitive. Realizing that this metamorphosis is slowly killing Rex, Batman sets out to find a cure. But Rex is only concerned about one thing: Sapphire Stagg and he would risk all of Gotham to be with her. But her father Simon Stagg holds secrets of his own and will do anything to keep them apart.
- Ra's al Ghul recruits all of the super villains Batman has brought down to eliminate Batman in exchange for control of a piece of the city. Batman races to find Ra's location and save both his partners and the entire city while Lt. Gordon and Barbara attempt to hack and disable the Ion Cortex once and for all.
Trivia: There are at least two Looney Tunes references in this episode: one near the beginning when Tobias Whale calls Professor Pyg "Porky", and later when Pyg calls Magpie "Tweety".
- Strange life-sized toy soldiers have started appearing all over Gotham... armed with real weapons! When Batman investigates, however, he discovers that they are not toys, but people trapped inside explosive shells. All the clues lead to a former mob accountant named Humphrey Dumpler who used to work for crime boss Tobias Whale, but went insane when Whale tried to silence him before he could testify. Now, Dumpty wants payback and the next person he's targeted is Lt. James Gordon.
- Six months after the blackout caused by the League of Assassins, newly appointed District Attorney Harvey Dent is trying to put a stop to the mask and cape crisis. Meanwhile, Batman finds himself being framed for an attempted attack on the life of Mayor Marion Grange and takes drastic action to find out who is responsible.
- Jason Burr steals the Ion Cortex for the League of Assassins as Lady Shiva brings Ra's al Ghul out of suspended animation. Batman, Katana, and Alfred then find themselves in a difficult situation as they battle the League of Assassins in a fight to save Gotham City from darkness. Batman is captured by Ra's al Ghul, while Katana and Alfred are left scared and alone.
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