Scarecrow's Alliance

Scarecrow's Alliance was a group composed of several criminals led by Scarecrow and The Arkham Knight, whose goal was to take down the Batman.

Leaders

 * Dr. Jonathan Crane/Scarecrow - Leader
 * Jason Todd/Arkham Knight - First commander of the Militia
 * Slade Wilson/Deathstroke - Second commander of the Militia, campaign overseer

Allies

 * Harleen Quinzel/Harley Quinn
 * Harvey Dent/Two-Face
 * Oswald Cobblepot/Penguin
 * Edward Nygma/Riddler
 * Garfield Lynns/Firefly- Freelance
 * Victor Fries/Mr. Freeze- Unwilling Ally
 * Simon Stagg - Former
 * Scarecrow Thugs
 * Arkham Knight's Militia
 * Arkham Knight's Drones

Between Arkham Asylum and Arkham Knight
After Scarecrow was brutally mauled by Killer Croc at Arkham Asylum, he began to plan his revenge on Batman. For countless months, Scarecrow wanted to attack Gotham City and unmask Batman. Scarecrow was approached by the mysterious Arkham Knight who wanted to kill Batman as well. The Knight pointed out that two men couldn't do it alone. It would taken an entire army to kill Batman. The Knight claimed he knew the Bat's tactics after studying him for years. If they wanted to defeat him, they would have to cut off all escape routes and take control of roads, skylines, and bridges. Scarecrow wanted to torture and then humiliate Batman in front of the public, while the Arkham Knight wanted simply to kill him. They decided to compromise after revealing the Dark Knight's identity and exposing him as a mere man, the Knight could execute him. Both Scarecrow and the Arkham Knight found a former assassin named Deathstroke who was known as the "toughest bastard who faced the Bat". Deathstroke had been chosen to oversee their campaign and serve as a backup commander if the Arkham Knight was done for.

It Started With a Meeting
After the Protocol 10 and the Arkham City incident, nearly every villain, henchman, and psychopath was released. This proved to be a prime opportunity for the mad doctor and his militaristic partner. Various members of Batman's rogues gallery were invited to a meeting at Arkham Asylum. They all were given an equal chance to kill Batman and fulfill each of their personal goals: Harley could get revenge for the death of the Joker, Two-Face could make his fortune and retire, Penguin could make huge profits by supplying every criminal with weapons, Riddler could finally defeat the his intellectually inclined foe, and Firefly was promised to burn down as much of the city as he wanted. Poison Ivy not so kindly rejected the offer, leading to her kidnapping.

Scarecrow also approached Mr. Freeze to personally capture Batman. Victor refused to do so, wanting only to develop a cure for his terminal wife, Nora. Crane decided to use the sword instead of the olive branch. He ordered his military advisors to send Militia to capture Nora's cryo-chamber and hold her hostage until Freeze captured Batman.

Arkham Knight Incident
On October 30th, Scarecrow unleashed his newest strain of Fear Toxin in Pauli's Diner, and threatened to release it throughout Gotham. Six million civilians were evacuated in 24 hours, but the city's criminals and supervillains stayed behind, leaving Commissioner James Gordon and the Gotham City Police Department outnumbered. Batman investigates Scarecrow's presence, and rescues Poison Ivy from a rooftop safehouse, where she was being held captive by Scarecrow's henchmen. Batman traces Scarecrow to Ace Chemicals, where he plans to disperse enough Fear Toxin to cover the eastern seaboard. Batman goes to investigate, but is confronted by the Arkham Knight. After fighting through the Knight's militia, Batman confronts Scarecrow. Crane reveals that the Arkham Knight has kidnapped Barbara Gordon. With Batman preoccupied checking on his friend, Crane is able to slip away with enough time to escape the blast radius.

Scarecrow's Plans
Knowing that Batman would go after him for kidnapping Barbara, the Arkham Knight has one of his men put on a voice synthesizer in order to trick Batman into following the wrong Armored Personnel Carrier (APC). While Batman chased the wrong APC, the Knight had Barbara moved to a more secure location. Scarecrow leaves to hide out on Stagg Airships and begins working on a device known as the "Cloudburst". Batman confronts Crane, but due to a fear gas hallucination, the Dark Knight is incapacitated. Crane escapes with the Cloudburst, the dispersal device he will use to flood the city in fear gas. Batman enlists the help of Ivy, who takes control of a large tree which develops giant flowers capable of neutralizing the toxin. As she is evolving the plant, they are attacked by drones. Batman is able to defeat the drones with Ivy's help.

City of Fear
Furious, Scarecrow ordered the Knight to activate the Cloudburst device, flooding Gotham City with fear toxin. The toxicity overwhelms Ivy, mortally wounding her. Batman finds that the Cloudburst was placed on the Arkham Knight's tank. The Knight is attacked and defeated, angering Scarecrow. The destruction of the Cloudburst leads to all of fear toxin being dissipated. Ivy dies after helping to clean up the toxin, having absorbed all of it into her body. In retaliation for this defeat, Scarecrow has James Gordon kidnapped and taken to Arkham Knight's HQ.

Knight Knight
The Knight confronts Batman in the tunnels under his HQ, revealing that he knows his identity and destroying the Batmobile. The Knight then stops Batman from saving Gordon and reveals his own identity as Jason Todd, the second Robin. Batman is bewildered because Todd was previously thought to have been killed by the Joker. Todd decided to kill his former mentor because Batman did not save him nor had the conviction to kill the Joker for what he had done. Batman defeats his former apprentice and attempts to convince Todd that he can be redeemed. In response, Todd curses Batman and vanishes while Bruce informs Alfred about Todd's survival. After Todd's defeat, Batman teams up with Gordon to arrest the Master of Fear.

Wayne vs. Crane
The duo use the HQ's elevator to reach the Scarecrow on the roof. Crane acts surprised and remarks that it is a miracle because "he doubted that he could make it happen". As Batman moves into arrest him, Scarecrow reveals that he has an ace up his sleeve. He has Barbara tied up and her father was asked to deliver Batman in return for her life. As ordered, the commissioner shoots his friend in the chest. However, Scarecrow becomes livid, revealing that he didn't want Batman simply gunned down. To "repay the favor", he throws Barbara off the roof. She is saved by Batman, who reveals that James purposely shot Batman in his bullet proof armor. He then proceeds to take her to GCPD Headquarters for safekeeping. The mad doctor becomes enraged stabbing one of his own men and injecting him with toxin. Crane then retreats to his secondary hideout on Arkham Island.

The Clown
While Batman was busy trying to stop Scarecrow, Harley broke into Panessa Studios, locked Batman out, and freed the three of the four people who were infected with the Joker's blood. Since Joker's blood was mutating them to be like the Joker, Harley wanted to join up with them and get her pud'n back. The Clown figured what better way to honor the Joker than letting his legacy live on in others. Batman and Robin worked together to defeat the three mutated Jokers, and returned them to their cells. Harley and her gang cornered Robin, and Batman snuck in under the grates, and took Harley out with a Floor Grate Takedown. After he and Robin defeated her thugs, Batman carried Harley to lock her in a containment unit.

The Lawyer
Two-Face's Gang tried to rob multiple banks of the evacuated city in an attempt to wear Batman out and to earn themselves and their boss enough money to retire. Harvey wanted to take the money because it belonged to the mob, while Two-Face just wanted the money in general. This way both personalities would be content. The Lawyer decided stay out of the spotlight and hideout at Hell's Gate Waste Disposal, coordinating robberies in both Gotham and Blüdhaven.

Batman learned of his disfigured foe's plan and went after his men at the Bank of Gotham's three branches. After Batman stopping the three robberies, Two-Face appeared in person, with multiple members of the Arkham Knight's Militia, as opposed to just his common street thugs. The Dark Knight worked his way through the bank, eventually taking them all out. After that, Batman took the disfigured D.A. to the GCPD Lockup.

The Gunrunner
Just as all the other villains had a specific role to carry out, Penguin's role was specifically to provide weapons and arms to the militia forces and the other villain crews, including Two-Face's, despite their mutual hostility toward each other. However, the Arkham Knight had ensured that there would be a truce between them and that Cobblepot would get the biggest pay day of his career.

Penguin was smuggling guns from Blüdhaven, the home of  Nightwing, to Gotham City. After interrogating Penguin for information, Batman is captured by two of Cobblepot's men. Nightwing shows up and helps Batman defeat the gang. To stop the flow of weapons, the Dark Knight destroys the Penguin's weapons cache. Nightwing helped him take out several other caches throughout the night.

In response to Batman's destruction of all of his caches, the Gunrunner kidnapped and planned to kill Nightwing as revenge. Batman soon came to his rescue and the two defeated Penguin's men, only for Penguin to hold Nightwing hostage at gunpoint just after Batman proceeded to rig the final cache to explode. Unfortunately for him, Nightwing escapes his grip and and he and Batman subdue Cobblepot before they blew up his weapon cache in front of him and knocked him out. Batman then imprisoned him in the GCPD holding cell. If Two-Face was imprisoned beforehand, Penguin said he should have told Scarecrow that it was a bad idea to involve him, only to be vaguely threatened by the scarred attorney.

The Genius
Riddler kidnaps Catwoman taking her hostage at the abandoned orphanage and sends Batman a message. He demands that he come to the orphanage or else Catwoman would die. Upon Batman's arrival, Riddler then revealed his line of robots to them. After they were destroyed, Riddler then informed them of the collar and challenged Batman to beat his riddles (being races and other puzzles) to free Catwoman with nine keys (actually ten) from the collar. During this time, Riddler also proceeded to improve on the robots to take into account Batman and Catwoman's respective abilities. This way if could not win intellectually, the Genius would have a way to physically eliminate them.

Eventually, Batman and Catwoman managed to beat the challenges and remove the collar, although Riddler ended up unveiling his Riddler Mech. After fighting, he then retreated, and stated that he'd only challenge Batman again after he had solved all 243 riddles throughout Gotham, thinking it would be impossible for the Dark Knight to accomplish such a feat. Upon Batman doing so, Riddler confronted his nemesis. He almost defeated Batman, but Catwoman returned and helped him defeat the Riddler Robots. This culminated in the inquisitive quizzler of queries' defeat.

The Arsonist
Batman encounters Firefly burning down the Bristol Fire Station. Batman chases the arson-prone insect across Miagani Island in the Batmobile. Eventually Firefly's jetpack ran out of fuel. This allowed Batman to directly attack Lynns, who managed to escape despite the damage to his equipment.

Instead of escaping Gotham, Firefly decided to continue with his assignment. Batman later crossed paths with Firefly at the Cauldron Fire Station. Batman chased the psychotic arsonist across Bleake Island in a second attempt to capture him. Again, Firefly's jetpack ran out of fuel, allowing Batman to attack him. Firefly was able escape yet again.

Even though he had been beaten twice, the arsonist could not resist burning down the final fire station, Otisburg Fire Station. Batman found the building on fire and confronted the arsonist once more. After Firefly's jetpack malfunctioned again, Batman was able to final take down the madman. He then commandeered Firefly's jetpack and it carried them both to the GCPD Lockup, where Lynns remained incarcerated for the remainder of the night.

The Iceman
Mr. Freeze became too preoccupied trying to salvage his research on Nora's illness to fight Batman. The Militia were sent in to remind the Iceman of his obligation to the Master of Fear. He was able to use his new wrist-mounted freeze ray to hold them off.

Coincidentally, Batman noticed Freeze's ship off the coast of Miagani Island. He confronted the Militia and was able to defeat them. He then traveled to the undercarriage of the ship where Freeze was working on salvaging his work. The Iceman decided to take the opportunity to capture the Caped Crusader. Batman told Victor that Crane had no intention of sparing Nora and that trusting him was his only chance.

Freeze relented, giving Batman a device to track Nora's cryo-chamber. The Dark Knight would find her while Freeze would continue to stabilize his research. However, the Militia anticipated that Freeze would betray them. So, they sent out a signal identical to the one used for Nora's capsule, hoping to ambush whoever came for her. Batman was able to defeat the soldiers and interrogated one into confessing that Nora is being held on a rooftop in Otisburg.

Batman informed Freeze of the ambush and Nora's location. Victor began to worry because if she was to be separated from the Cryo-Genator for too long, she would awaken. Batman reassured him that he would find Nora in time.

Batman defeated all of the soldiers guarding Nora and decided to examine the capsule to see if it was still operational. Suddenly, the latch opened, freeing Nora Fries from ten years of suspended animation. She confessed that she had been conscious the entire time and was sickened by what her husband had become. Freeze then called the Dark Knight to ask how the mission was going. Batman told Freeze that Nora was awake, causing the Iceman to panic, asking Batman to put her back in the cryo-chamber. Nora spoke to her husband for the first time in a decade, explaining that she didn't need a cure, just him. While they were speaking, the Cryo-Generator on Freeze's ship overloaded, causing a massive explosion, freezing Gotham Bay and causing it to snow across the city.

Batman and Nora rushed to Freeze's ship in order to save him from the Militia's drones. Freeze and Batman were able to defeat many of them, but the Militia just had more on the way. Freeze realized he had two choices: detonate his Cryo-Generator and lose his research or let the Militia kill him and his wife. Nora plead with her husband to give up the research and he relented.

After using his Cryo-Generator as a bomb, he destroyed all of the drones, only to lose his life's work. He and his wife decided to leave Gotham and spend Nora's last days in peace before she would die. Batman decided to let Freeze go and took off in the Batwing.

The Assassin
With the Knight defeated, Batman receives contact from the current leader of the Arkham Knight's Militia; Deathstroke who wanted to finish off Batman with advance payment even without Scarecrow or the Knight's help. Deathstroke owns the remaining APCs, watchtowers, road blockades and bombs in Gotham City. After destroying Deathstroke's forces, Batman and Deathstroke go face-to-face at Grand Avenue. The assassin can not help but cheat. He goes into a fortified tank and calls the Militia Commander to send in as many Cobra Tanks as possible. After destroying all of his opponents "toys", Batman confronts Deathstroke. Batman is able to destroy the juggernaut of a machine and Deathstroke comes out to fight. The Dark Knight subdues the one-eyed assassin and takes him to the GCPD Building. As Batman locks up the assassin in a cell, Deathstroke warns the Detective that he will be free very soon.

Assault on GCPD
With many of his subordinates and his top assassin in prison, Scarecrow decides to attack the police head-on. His plan is to invade the police station, slaughter every officer, and free his men. He sends several militia to shut down power to the building. Batman is able to activate the back up generator. Scarecrow sends dozens of drones to GCPD to wear them down. Oracle is able to find a flaw in the drones' systems and tells Batman how to exploit them. After destroying the drones, Scarecrow sends helicopters to the roof of the building in order to use the elevator to sneak in. Barbara uses the electrical systems on the roof to help Batman defeat the militia and the Brutes.

Final Act
With all of his allies defeated, Crane pulls the last straw. He uses Gordon to access Panessa Studios and his men kidnap Robin. He relays a message to his nemesis, saying that in return for his surrender, he will release the two hostages. Batman decides to do so, leaving his weapons in a storage depot in Kingston and going into an unmarked van. The van takes him to Arkham Asylum with the mad doctor ready to operate.

Scarecrow straps Batman to a gurney and takes him into the Arkham Mansion, where he has set up a camera that is being remotely broadcast to all media outlets. He orders Gordon to take off the Batman's mask. When Gordon refuses, he shoots Robin in the abdomen and refuses to give him medical attention unless he complies. Reluctantly, the commissioner removes Batman's mask, revealing his identity as Bruce Wayne to the world. He is surprised that for years he was being defeated by a rich orphan. Then, he begins with the torture that he was so sadly deprived of. He injects a massive amount of toxin into the defeated hero, sending Wayne into a nightmare where he succumbs to his Joker Infection and destroys Gotham.

As Crane addresses the city, saying that Gotham no longer has a hero, Batman uses his will power to suppress both the toxin and the Infection. After addressing the city, he injects Wayne again to show that he is just a man, not the symbol everyone thinks he is. However, it is ineffective. In a twist of irony, all of the years of injecting his enemy with toxin made the Bat build up an immunity coupled with his will power has made the toxin infective. Jason, now working with Batman and operating as the Red Hood, rebels against his boss and saves his former mentor. The Dark Knight takes Crane's hand and forces the doctor to take a dose of his own "medicine". This sends Scarecrow into a perpetual state of fear, seeing nothing but bats. After the longest night of his life, Gordon knocks Crane out and arrests him. Gotham's hero delivers the fearful doctor to GCPD Lockup.

Knightfall
By the end of the night, the entire alliance, minus Todd and Fries, was arrested and placed in jail. They were all charged on multiple counts of attempted murder, kidnapping, conspiracy, and many other charges. The Master of Fear was reduced to a sniveling, crippled old man. Their mission failed, their henchmen arrested, their leader broken and their purpose ruined, Scarecrow's alliance became well and truly defeated.

Trivia

 * All three leaders wanted to attack Batman but for different purposes.
 * Scarecrow: Wanted to unmask the Batman so that his legend died.
 * Arkham Knight: Wanted to kill Batman after being tortured by the Joker for over a year at Arkham Asylum.
 * Deathstroke: Wanted to kill Batman for money and to get revenge for being beaten by him during Arkham Origins.