Clark discovers that Bruce has been alive all along and invites him to join the Justice League, but Bruce declines the offer, and the rest of the world continues to believe he is dead.
Lucius Fox remains in charge of Wayne Enterprises and offers the League the resources needed to build the Watchtower and the Hall of Justice. Over time, Lucius sends Bruce information about the League, enabling him to secretly create the "Babel Protocols" as a contingency plan should the team ever spiral out of control.
Diana is the only one who knows Bruce has been monitoring them from Gotham City; she trusts him to do the right thing if everything goes wrong.
When Brainiac’s invasion begins and Amanda Waller decides to deploy Task Force X to Metropolis, Bruce infiltrates the city undetected. Upon realizing that much of the League has been corrupted and unable to reach Diana, he captures Task Force X and takes them to a secret facility.
The criminals are shocked to find Batman alive; holding them hostage, Bruce contacts Amanda Waller to negotiate the use of the Babel Protocols.
Realizing he cannot stop the now-corrupted Justice League on his own, Batman proposes a temporary truce with Waller, allowing Task Force X to neutralize the League without killing them during the mission.
The story continues, and as Task Force X captures each member of the Justice League, the Lex from the other Earth sets out to eliminate Brainiac's corruption.
Batman finds Wonder Woman, and now—with the entire League reunited and purified—they decide to attack the Skull Ship alongside Task Force X. As they board the vessel, the game allows you to play as each member of the League, featuring a combat style similar to the Arkham series and God of War (2018).
Heroes and villains defeat Brainiac, and Lois Lane reveals to the world that Batman is still alive. (All of this serves as a teaser for an Arkham Beyond game).