As for the plot I came up with, it's definitely influenced by the Chuck Dixon era of Batman, with elements like the Dick Grayson Cop & Stephanie Brown as Spoiler.
Gotham:
Story (Prologue 1):
The game would open with Jonah Hex in an old western stylized Gotham, where he would be saving Amadeus Arkham from a group of assassins with Hawks on their uniforms. A horse and carriage chase would lead Hex to the construction site of the Arkham Asylum, where he would find a painting on the wall of a Bat consumed by flames, surrounded by Hawks. At the construction site, Hex would meet the first Azrael of the Order of St. Dumas, who would tell him that one day, Gotham’s Dark Knight would fail.
Story (Prologue 2):
Bruce Wayne, aka Batman, would be having a nightmare about the first time he meet the Joker, back when he was the Red Hood. As Batman, he was responsible for turning the Red Hood into the Joker by accidently knocking him into a vat of chemicals. At this point, the dream begins to mix with the recent death of the Joker and he awakens to find Dick Grayson, aka Nightwing, and Tim Drake, aka Robin, in his room. Dick is dressed in a Gotham City Police Department uniform and the two of them are there to inform Bruce that he’s wanted for the murder of the mayor that night; Dick was on shift when the call went out for Bruce’s arrest. The three of them begin to move through the mansion, getting down to the Bat cave, which Bruce reluctantly blows up on the recommendation of Dick and Alfred, so the GCPD can’t find out his identity. Alfred distracts the cops, long enough for Bruce/Dick/Tim to activate the self destruct system. As the Wayne Manor/Bat Cave blows up in the background, the 3 bat members go their separate ways.
Story (Act 1):
Batman- Bruce Wayne’s story would start with him confronting Jim Gordon, who is now aware of his identity as Batman. Bruce and Gordon decide to team up, keeping in radio contact, and Batman investigates the scene of the Mayor’s murder. While he is there, he is shot with a dart full of Scarecrow toxin and he begins to hallucinate, seeing the Red Hood, confused on how the Joker is still alive. Batman gives chase, but the Red Hood continues to elude him and taunt him in the process. His voice is demonic, so Batman can’t tell if it’s really the Joker. The Red Hood leads him to the ruins of Arkham Asylum, where Batman comes across the painting from the Prologue 1. Then he runs into Azrael (from Arkham City), who stabs Batman through the chest with a flaming blade and tasks Batman with saving the life of the condemned. At the end of the chapter, Bruce is told by Gordon that there is prison break outs all over and he tells Gordon to send Dick Grayson to deal with it, since he is busy. At the same time, Bruce is confronted by Man-Bat, who is supposed to kill him to be spared by the ‘Hawks’. Bruce defeats Man-Bat after a fight in the sky and discovers trace elements of a substance found only atop Wayne Tower.
Nightwing- Dick Grayson returns to the Gotham City Police Department, that is over flowing with criminals, to see if he can find any evidence on the Bruce Wayne/Mayor case. All the prisons are filled to the brink with criminals, since the events of Arkham City. Dick Grayson is actually there to collect his gloves/gauntlets which he left behind after a ‘fight’ with Huntress a couple nights back. While Dick is at the police station, a low life criminal named Desmond Miles is complaining about something Two-Face injected him with, while the cops are bringing him in. The serum Two-Face injected Miles with turns him into Blockbuster, whom Dick has to fight in cop uniform, using two night sticks in place of his Escrima sticks. Blockbuster causes a break out through the cop station and takes out nearly all the guards, but Dick. Dick has to fight his way through the station and finally takes down Blockbuster. After suiting up as Nightwing, Dick gets called to the penitentiary, the big prison in Gotham, to deal with the break out by Gordon. As he’s leaving, Azrael stabs Dick through the chest with a flaming sword and tasks him with saving the lives of the innocent.
Robin- Tim Drake decides to hit the streets to see if he can scour the criminal underbelly to find a connection to the Bruce Wayne/Mayor case. This leads to him coming across girlfriend Stephanie Brown, aka Spoiler, who reveals her father, Clue-Master, might have played some part in it.
Clue-Master left a map to Stephanie, to see if her daughter was smart enough to locate her, which Tim takes. The two part terms, warning each other to be careful as the break outs all over Gotham occur. Clue-Master has left behind several hints at different locations that Tim will have to go to and solve, before being able to track Clue-Master down to his hiding place. Hacking into his computer, he finds an email, telling Clue-Master to meet up with the others at the Scarecrow’s hideout.
Clue-Master left a map to Stephanie, to see if her daughter was smart enough to locate her, which Tim takes. The two part terms, warning each other to be careful as the break outs all over Gotham occur. Clue-Master has left behind several hints at different locations that Tim will have to go to and solve, before being able to track Clue-Master down to his hiding place. Hacking into his computer, he finds an email, telling Clue-Master to meet up with the others at the Scarecrow’s hideout.
Story (Act 2):
Batman- When Bruce gets to Wayne Tower, he is confronted by the Red Hood again. This time, Red Hood talks to Bruce, revealing he knows his true identity and asks him how many employees work at Wayne Tower, even late into the night, before revealing the answer and telling him he has to save them all, as his men have infiltrated the tower. After Bruce saves them, he confronts Red Hood, whose physical prowess is as refined as his own. Red Hood taunts him by showing him images of incapacitated Dick and Tim and gives him them their location, allowing Red Hood to escape. However, it’s a dead end and Bruce comes across a bloody crowbar at the location, with an invitation to the base of the Hawks.
Nightwing- This segment opens with Harley Quinn and Poison Ivy confronting Selina Kyle in her prison cell. Ivy tells Selina to get over her crush on Batman, he obviously put her in a prison cell for a reason and that she escape and help them find Two-Face, who was the last person to have seen Quinn’s baby. Selina reluctantly agrees and Ivy mentions that one of her plants saw one of Batman’s little birdies coming and that they could use him to their advantage. When Dick arrives at the Penitentiary, Dick has to fight his way through criminals like Killer Croc. During this time, Barbara manages to get a hold of Dick over his radio and the two communicate and keep each other updated on events. Before he gets to Two-Face, Dick reveals he knows the Sirens are following him and he fights Ivy and Selina while Quinn continues to hunt down Two-Face for her child. They nearly beat him, but Dick convinces Selina to help him and they take down Ivy. Two-Face reveals himself then and takes out Selina, but before he can take down Dick, Harley Quinn shows up. The three fight one another, but Two-Face reveals he gave the baby to someone with a vendetta against Joker and she assumes it is Batman and attacks Dick because of that. Two-Face takes out Harley and Dick, telling Dick he has an old friend for him to meet.
Robin- Tim Drake arrives at the villain hide out, when Alfred manages to get a hold of him over the radio. Alfred managed to escape cop custody by playing the part of a mourning parent for Bruce and Tim has to fight his way through the bosses, without Batman, a moment he’s been training for. Alfred gives Tim advice on how to take down each boss and although he emerges victorious against the likes of Bane, Scarecrow, and Riddler, he is severely beat down by the events and when he sees Bruce, he forgets his mission. Tim tries to talk to him, only to have Bruce take him down, when in reality Bruce is actually the villain Hush.
Story (Act 3):
Batman- Bruce has discovered the location of the Hawks and goes about trying to defeat as many of them as possible, while trying to save their hostages. At one point, the order goes out to kill all the hostages and Bruce has to abandon all stealth and fight his way to the head of the organization. It turns out the Red Hood wasn’t the Joker like Bruce had suspected, but Jason Todd, the second Robin, who the Joker beat to death. Bruce tries to reason with Jason, but Jason doesn’t listen to Batman. Jason believes he has to rule crime to save Gotham, but he has a personal vendetta to deal with first; Joker’s baby, who he intends to kill. Bruce has to decide whether to stop Jason or save the baby, who is clearly not a normal child. In the end, Bruce saves the child and Jason escapes. Azrael appears to tell Bruce that he failed his mission to save Jason Todd, the condemned. As a result, Gotham City will burn and Bruce will find himself at the Gates of Hell before the end.
Nightwing- When Dick comes to, he’s confronted by James Gordon Jr. who reveals he’s working with the Red Hood to take down Batman and his family. Dick and James were childhood friends, but the Joker poisoned his mind and now he wants Gotham to burn. James reveals he knows it’s Dick beneath the mask and tells Dick that he has men planting bombs all over Gotham, and has sent a group of trained Hawk assassins to kill Barbara. Dick manages to break free after James leaves, but he has to choose between Barbara and saving Gotham. He can’t get a hold of anyone else, as he begins to take down the bombs and he manages to get one final call to Barbara, telling her he loves her, before the assassins reach her building. Dick takes out all the bombs and finds James who he nearly kills in anger, but Jim Gordon Sr. stops him and they take his son into custody. Azrael appears to tell Dick he succeeded in saving the innocent and as a result, he saved Barbara from her attackers; Dick and Barbara embrace.
Robin- Tim Drake is awoken by Hush, who kills Clue-Master in front of him and tells him that they know Stephanie helped him and have plans to kill her as well. Hush injects Tim with a needle of Scarecrow toxin and then sets him free, using the identity of Bruce Wayne to mess with Tim’s head. Tim eventually overcomes the toxin and takes out Hush, when Azrael appears with the cops and tells Tim he managed to save the life of the convicted, clearing Bruce’s name. Tim doesn’t stick around though, trying to get to Stephanie as fast as he can. He manages to save her, but has to tell her that her father is dead, comforting her as she weeps.
Story (Epilogue):
Bruce, Tim, and Dick, all in costume, look over Gotham City as it begins to burn, nearly all of the criminals on the loose. Bruce thanks Tim and Dick for their help, but his final mission he will have to go it alone. Dick and Tim tells Bruce that he is wrong, that all across Gotham more will rise to the occasion in Gotham. We then see Huntress, Jim Gordon & Cat-Woman fighting criminals, and Barbara Gordon passing the Batgirl mantle on to Stephanie Brown. Bruce tries one last time to convince them to leave, but they refuse and the three vigilantes drop down into Gotham, ready to face what comes next. 