The Shadow War

The Shadow War was a civil war that began after Protocol 10 between rebels and loyalists of the League of Assassins.

Prelude
While Ra's al Ghul was gloating that Protocol 10 would be a success, Hugo Strange, his disgraced minion, activated Protocol 11. Protocol 11 caused Wonder Tower to explode, although Batman and Ra's were able to barely escape. As Batman was about to arrest the Head of the Demon, he took his sword and committed suicide mid-air.

After the death of Ra's al Ghul, a group of loyalists took his body and sword. They attempted to resurrect their master with an impure Lazarus source. This only brought him back as a barely conscious zombie.

Insurrection
Ra's daughter, Nyssa Raatko, decided that her father should be put out of his misery. The Loyalists refused, asserting that their master would return to eventually full strength. For Nyssa, eventually was not good enough. So, she created a rebel faction in order to prevent the resurrection of her father and to ensure that no more innocents would be hurt in the crusade for justice.

Shadow War
On Halloween Night, Alfred alerted Batman that a GCPD officer just witnessed two "crazy ass ninjas" fighting on Miagani Island. Batman investigated and found two dead ninjas wearing different outfits and a sword with blood on it. He followed the blood trail to Elliot Memorial Hospital. He noted that neither Ra's nor the League had been seen since the body of Ra's disappeared in Arkham City. At Elliot Memorial, Batman saw new members being trained by a member of the League. He learned that there were two factions of the League: the Loyalists and the Rebels. Batman learned that the Loyalists had returned to Gotham, in the hopes of fully restoring Ra's. The Rebels wanted to ensure that the Demon's Head was never brought back. Batman was tasked by the Loyalists with finding a pure source of Lazarus chemicals to heal Ra's or else the war between the assassins would destroy the city.

Batman used the Batmobile to track the source of Lazarus under Panessa Studios. After finding the last pool of Lazarus in Gotham (and possibly on Earth), he was attacked by the Rebels. After defeating them, he took a sample of Lazarus and attempted to destroy the rest with Explosive Gel. He was then stopped by the leader of the Rebels, Nyssa Raatko. Nyssa then asked Batman to destroy her father's life support and let her take over, before detonating the Explosive Gel herself.

When Batman returned to Elliot Memorial, Alfred tried to convince him to let the Demon's Head die. Batman contemplated his options as he headed for Ra's life support. If Ra's were to die, the assassins would leave Gotham. If he did disconnect Ra's from his machine, he would be breaking his no kill rule.

Outcome
If Batman decides to give Ra's the Lazarus cure, he injects him with the pure Lazarus. Immediately after, the Rebels attack intent on killing Batman for betraying them. After Batman defeats all of the Rebels, he is attacked by Nyssa asking why he would help a man as evil as Ra's. Ra's returns to strength and accuses his daughter of being a traitor. He then slashes her in the stomach, leaving her to bleed out. Batman then attacks Ra's, but Ra's is able to steal one of Batman's Smoke Bombs and escapes. Batman consoles Nyssa in her final moments. Alfred then tells Batman that he has stopped a terrible war and he would not have to worry about the League for a while because it will take time for Ra's to heal and the Rebels have scattered. At GCPD, some of the Rebels are placed in holding cells and call the Dark Knight "traitor". Their weapons and uniforms are then placed in the Evidence Room.

If Batman decides to destroy Ra's life support, he uses two Batarangs to destroy the machine, which causes the Loyalists to attack intent on killing Batman for his betrayal. After Batman defeats the Loyalists, Ra's tries to crawl away. He is then confronted by Nyssa, who is disgusted by what he has become. She attempts to deliver her father a killing blow, but she is stopped by Batman. She tells the Dark Knight that her father will die in a few days anyway. She fulfills her promise by taking control of the League of Assassins and leaving Gotham forever. Batman takes Ra's to the GCPD. After locking the former Master of Assassins away, Ra's thanks the "Detective" (Batman) for doing the right thing. After six centuries, the Demon's Head is ready to pass away peacefully. At GCPD, some of the Loyalists' weapons and uniforms are then placed in the Evidence Room.

Rebels

 * Nyssa Raatko
 * Rebel Assassins
 * Rebel Initiates

Loyalists

 * Ra's al Ghul
 * Loyalist Assassins
 * Loyalist Initiates

Trivia

 * The mission Shadow War was proof that the civil war was indeed The Shadow War.