Batman and Catwoman go to the Batcave to obtain the weapons Batman has prepared against the Justice League, hoping they can be used against the Crime Syndicate. Afterwards, they make their way to the Wayne Enterprises building, where they come across Lex Luthor, Bizarro, Captain Cold, Black Manta and Black Adam. However, both groups are attacked by Power Ring, a member of the Crime Syndicate, and his henchmen. Batman uses a Sinestro Corps ring to fight Power Ring, but the ring's charge quickly runs out and Power Ring destroys the ring. But in that moment, Sinestro appears to confront Power Ring. Batman, Catwoman and Luthor's group combine forces and defeat Blockbuster, Copperhead, Giganta and Shadow Thief. Luthor also convinces Deathstroke to join their group; while Sinestro, who has killed Power Ring, joins them as well.
Seeking retaliation for Ivy's manipulation, Catwoman offers information on her whereabouts to Batman in exchange for a kiss and a tenuous romance blooms between them. Batman and Catwoman follow Poison Ivy to Metropolis. Batman finds Lex Luthor, now a probationary member of the Justice League, and asks for information on a delivery list of an ethylene compound to track down Ivy's location. There they find Ivy has taken control of Superman and she commands the Man of Steel to kill Batman and Catwoman. Batman observes that Superman is subconsciously resisting Ivy's influence, holding back on his attempts to kill both of them. Using knuckledusters made from Kryptonite, Batman stalls Superman while Catwoman lets Lois Lane fall from the Daily Planet building. Superman breaks free of Ivy's control to save Lois. Batman, Superman, and Catwoman work together to capture Ivy, who reveals that she was being manipulated by a mysterious foe called Hush.
In Final Crisis #6, Batman confronts Darkseid in the villain's bunker. He states that he will make an exception to his "no firearms" rule and shoots Darkseid using the bullet that killed Orion and hits Darkseid. As Darkseid dies he fires the Omega Sanction (which traps its victim's soul in a series of alternate lives, each worse than the one before it), from his eyes, and hits Batman. Before the Omega Sanction hits Batman he silently says, "Gotcha". It is unknown if ' Batman knew Darkseid shot the Omega sanction or he knew it was coming and accepted his fate. (Morrison notes that Batman's use of the gun is symbolic as “the root of the Batman mythos is the gun and the bullet that created Batman. So, Batman himself is finally standing there to complete that big mythical circle and to have the image of Batman up against the actual personification of evil and now he's got the gun and he's got the bullet. It seemed to me to work.") At the close of the penultimate issue in the series, Superman returns to Earth from the 31st century, where he was given access to the reality-altering Miracle Machine by Brainiac 5 of the Legion of Super-Heroes. In a fit of desperate rage, Superman attacks Darkseid's bunker, finding Batman's charred corpse within. The Dark Knight is seemingly dead. However, the Omega Sanction does not kill its victims: instead, it sends their consciousness traveling through parallel worlds, and at the conclusion of Final Crisis, it is made clear that this is the fate that has befallen the still-living Batman, as he watches the passing of Anthro in the distant past.
While the Crime Syndicate imprisons the Justice Leagues inside the Firestorm Matrix, Batman, Catwoman and a critically injured Cyborg escape in a sewer system and go to S.T.A.R. Labs. There, they find Doctors Silas Stone and Thomas Morrow. As Batman and Catwoman explain their situation, they discover the Crime Syndicate has taken over the world and revealed Nightwing's identity. Batman decides to find Nightwing.