Shadow War

Shadow War is a Gotham's Most Wanted mission in Batman: Arkham Knight. The Season of Infamy DLC and 27% of City of Fear is required to unlock the mission. The villains are the League of Assassins Loyalists, who intend to resurrect Ra's al Ghul in the midst of a civil war.

Plot
"Sir, there's been a sighting of the League of Assassins." "The League? You're sure?" "I'm pretty sure it's the League, sir. Although the reporting office only stated seeing and I quote "crazy-ass ninjas"."

- Alfred informs Batman the night got even worse Alfred notifies Batman that two League Assassins have been spotted ontop of a building, fighting. After investigating, Batman follows a blood trail, leading to the Elliot Memorial Hospital, leading him to the loyal League Assassins. After defeating them, Batman powers up the Hospital to gain access through the elevator. He encounters a locked door with switches beside them. After pressing the switches in the correct order, Batman gains access to the Lazarus Chamber, and encounters a zombie-like Ra's al Ghul, sitting on a throne-like seat, with Lazarus streams flowing through his blood, according to Batman, are the only things keeping him alive. Two assassins hold blades at Batman's throat, about to kill him, but are stopped by another assassin, who explains to Batman that he has no choice but to heal the Demon's Head. If the stalemate continues, Gotham will be destroyed. After locating the Lazarus Pit, Batman, about to take some of the fluid, is ambushed by Rebel Assassins. After defeating them, he is to come face to face with Nyssa Raatko, the other daughter of Ra's Al Ghul. Before detonating the pit, Nyssa steals Bruce's detonator, and explains to him that her father, or what's left of him, needs to be killed, once and for all. Batman then heads back to the chamber, and confronts Ra's Al Ghul. This is where the player is given two choices. To either destroy Ra's' streams that are keeping him alive, or administer the cure, healing him.

If you pick choice A:, you then fight the League of Assassins loyalists while Nyssa prepares to execute her father once and for all, but Batman ultimately intervenes and stops her, intending to take Ra's to justice. Nyssa concedes and gathers the League of Assassins under her command to leave, reassuring Batman she will keep her promise that they will never return to Gotham. Batman takes Ra's to GCPD, where he is locked up for what remains of his last life to pay for his crimes; he claims to be proud of Batman. Some fans interpreted this as Ra's being proud of Batman for breaking his only rule, while others point out that Batman's choice to not cure Ra's is similar to his choice in Batman Begins, where he states, "I won't kill you, but I don't have to save you".

If you pick choice B:, you cure Ra's, and fight the Rebel Assassins, then have a fight with Nyssa herself. Ra's then emerges from his throne, picks up a sword and fatally strikes Nyssa across her side, calling her a traitor. He attempts to fight Batman, but, still not completely healed, is quickly overpowered; Ra's then uses a cloud of smoke to escape, unpunished, and fully recover. Batman offers to heal Nyssa with the remaining Lazarus, but she refuses to follow her father's path. When she dies, Batman closes her eyes and leaves. Alfred contacts Batman to say that both factions have all left Gotham, with Ra's gone and with no idea how long it will take for him to fully heal Alfred tells Batman that he's managed to avert a war between both sides of the League of Shadow, all while sticking to his moral code and not killing Ra's, but in the process, getting the honorable Nyssa murdered.

Characters

 * Batman
 * Alfred Pennyworth (Voice and hologram only)
 * Ra's al Ghul
 * League of Assassins Loyalists
 * Nyssa Raatko
 * League of Assassins Rebels
 * Talia al Ghul (referenced only)
 * Thugs (Only by following the Blood Trail)
 * Hugo Strange (referenced in one of the tapes)

Achievements/Trophies

 * The Demon Lives Again!  – Follow the Assassin’s Trail
 * Daughter of the Demon!  – Discover the Lazarus Pit
 * Ashes to Ashes  – End the League of Assassins’ War

Trivia

 * For the first time, the mission shows the interior of the Elliot Memorial Hospital.
 * Inside the hospital is the body of the first victim of the gas for the Scarecrow early in the game, the waitress Sharon Jones.
 * The man who also interrupted Officer Owens' dinner also appears dead later before making the choice.
 * One of the morgue lockers on the same wall as that of waitress Sharon Jones has the name Talia al Ghul listed; the door is slightly ajar, and the view inside is obscured by the escaping condensation, but switching on detective mode reveals it to be empty. Her body is nowhere to be found.
 * Hanging from a locker door inside the hospital is a lab coat with a name tag reading Bradford Thorne, the original name of villain Crime Doctor.
 * Inside the hospital is a Wanted poster for Dr. Linda Friitawa, aka the villain known as Fright.
 * This is the second side mission in the Arkham series to have multiple outcomes, the first being Heir to the Cowl.
 * In this case you must choose whether to side with Nyssa and preventing Ra's complete revival or side with Ra's by reviving him and getting Nyssa killed.
 * It's also the only mission in which the ending is debatable. While some might find Batman stopping a resurrection and cutting the life support the same as straight up killing someone as the evil outcome, others counter by saying that saving Ra's and allowing him to kill his daughter was the evil outcome.
 * The mission is the first and only time that Alfred swears in the series, although he is quoting a reporting officer. He describes the assassins as "Crazy-Ass Ninjas".
 * This mission marks the first and one of the few times Alfred has suggested killing any member of Batman's rogue gallery. He points out that Ra's is already dead and being forced to live artificially; he also adds Nyssa is more reasonable than Ra's to encourage Batman to deny Ra's a full revival.
 * Choosing not to revive Ra's and letting him finally die in GCPD custody is reminiscent to his death scene in the film Batman Begins. Batman says to Ra's that he won't kill him, but he won't save him either and leaves him aboard a train car that is about to crash and explode. Coincidentally that the film also had Gotham enveloped in a cloud of fear gas.
 * This scenario with Ra's heavily mirrors that of Joker's at the end of Arkham City. Both were dying and needed Batman for a cure to save their lives. If the player chose to let him die, Batman even carries Ra's the same way he did with the Joker.
 * Some would argue then that it would make more sense if Batman did save Ra's as he told the Joker he would have saved him. This is a subject brought up by the Joker hallucinations as well as Bruce fears that he was wrong and just couldn't admit it. This could then be seen as him proving himself by standing by his claim.
 * Additionally, Bruce's morals is not just about the "no-killing" rule. As the son of doctor Thomas Wayne, he values all life which is why he saved Joker from falling in Origins. It is the basis of his relationship with the Joker (who became obsessed with him soon after) and Ra's (who's differing philosophy and methods caused them to be enemies). By letting Ra's die, this would still be a departure from what made Bruce, what made Batman who he is. Even Nyssa admits, it is what made Talia love him.
 * Alfred's comment on the completed mission changes based on the outcome.
 * If Batman gave Ra's the Lazarus, Alfred will try consoling him about inadvertently causing Nyssa's death by explaining that both factions of the League fled Gotham; he also will add that Ra's will be taking a long time to recover. If the player checks the completed mission on the selection screen, Alfred will congratulate Batman on not breaking his rule to never kill.
 * If Batman denies Ra's the Lazarus, when the player checks the completed mission on the selection screen, Alfred will say Nyssa is now in control of the League and say it's a good outcome.