I am a strong supporter in the fact that if this is a trilogy then tie all three movies together, and not just based off the main character in this case Batman.
The opening scene Ive envisioned would be a back story on Ras Al GHul and The League of Shadows. Ras before finding Wayne had previously attempted a similar recruitment of someone with a very similar upbringing as Bruce Wayne but he failed and instead of creating a hero he created a cunning, vicious, and untraceable villain
Batman 3-The Dark Victory
Bruce will struggle hard with the consequences of being Batman and will vow to give up, he must first replace Harvey Dent himself or find someone that can do it and support them both as Wayne and as Batman. Batman has become something of a loner, distancing himself from Gordon and anyone else who might also have their lives torn apart like Dent did. Bruce Waynes struggle in TDK was to support Harvey and have him take over as the crime fighter of Gotham so he could let go of Batman, in this movie he will find out how much he and Gotham need Batman. In the beginning, Bruce begins to shift more of his focus on cleaning up Gotham from a humanitarian angle using Wayne Enterprises and his wealth to fight the good fight in the public.(Similar to his father Thomas Wayne) Things take a turn for the worse when Wayne Enterprises is accused of violating labor laws and economic scandal. Bruce will have the fight of his life as he is challenged as both Batman and Bruce Wayne by Roman Sionis. This is the Black Mask an older man , rich, a rogue member of the league of shadows and his False Face Society a ruthless gang of disfigured members who have all been tortured and brainwashed. Black Mask's most important weapons are fear and intimidation. He is known for his brutal and sadistic torture techniques, especially on the face. Black Mask also uses his connections to gather information on his enemies, and then hits them at their weak points, such as family and friends. He was the crime lord of Gotham city for many years as an undercover businessman and was the original target of Ras al Ghul., Following Jokers lead, the costume villains band together to go to war with the mob, the police and the Batman, trying to stake their claim as Gothams new criminal fraternity. Meanwhile, in Gotham City, the final remnants of the Falcone/Maroni crime families huddle together to defend their shrinking empire against the wave of costumes that have invaded Gothams underworld. The Black Mask uses to his advantage the fact the Batman is now public enemy number one and the suspect of the murders committed in the Dark Knight. Reese, The employee from TDK who found blueprints for Tumbler (BATMOBILE) is found murdered, and Batman is framed, thought to be trying to protect his identity. This leads to an even greater pressure from the city for Gordon to capture Batman.
A new and mysterious female assistant D.A. emerges Talia Head and sparks the interest of Bruce Wayne and the public, she is secretly Talia al Ghul REMEMBER RAS LINE FROM BEGINS WHERE HE SAID THE LEAGUE HAD INFILTRATED EVERY LEVEL OF GOVERNMENT IN GOTHAM. She is a complex character, not quite heroine nor villainess but more of an anti-hero. Talia has brought a team of the remaining League of Shadows Warriors to Gotham City to hunt down the Batman and force him to join them or pay for her fathers death.
The Joker (in the eyes of Roman Sionis) was simply a pawn used to move in on the Falconne family, unseen in TDK was The Black Mask meeting secretly with the Joker unknown to Sal Maroni but after the Jokers capture he recants on his offer to the Joker and plans his assassination while in Arkham. He sees the Jokers purpose was served as he drove the Batman from hero to vigilante in the general public (WHO LET THE DOG OFF THE LEASH), and left the structure of the Mob weakened for his take over. The Black Mask is secretly also a wealthy business man and has the pull to push around Bruce Wayne and also fabricate documents and information. His Intel is unparalleled, he nearly completes a hostile takeover of Wayne Enterprises, and he is a master criminal strategist with vast amount of resources. The Black Mask and his gang of disfigured costume freaks infiltrate Wayne Enterprises and in an attempt to take over the building murders Lucious Fox who he sees as the brains of the executive board, framing Batman again in the process. Behind the near hostile takeover of Wayne Enterprises and death of Lucious Fox , Batman goes full fledged vigilante. Still wanted by the police and the mayor Batman takes the fight right at Black Mask using every resource he has left to topple the newly crowned king of the mob.
Gordon discovers he must find a way to get info out of the Joker, while in Arkham he is receiving treatment from a new doctor Dr. Harleen Quinzel who turns out to be an operative of the Black Mask. The Black Mask is determined to kill the Joker to conceal his identity but the operative does a double cross, and frees the Joker. He then kidnaps Commissioner Gordon and taunts him with enlarged photographs of his wounded (family member), in an attempt to prove that any normal man can go insane after having "one really bad day." The Joker ridicules him as an example of "the average man," a naïve weakling doomed to insanity. Again giving an explanation of the scars on his face to Gordon with a knife pressed to the inside of the Commissioners mouth "something like that happened to me you know...I'm not quite sure what it was. Sometimes I remember it one way, sometimes another. If I'm going to have a past, I prefer it to be multiple choice!" The Joker knowing the true identity of Black Mask and his intent on taking over Wayne Enterprises destroys the Wayne tower to announce to Gotham that he is again free and that terror has returned to Gotham while using his influence over the false face society to take down whats left of the Falconne/Maroni family and overturn the Gotham Police Department and create CHAOS in the streets of Gotham with no rules and no laws.
Batman has to stop the Joker while struggling with the conflict of continuing his life as both Batman and Bruce Wayne or accepting the offer from Talia who is determined to have Bruce lead The League of Shadows. In order to stop the Joker and his gang of freaks he agrees to lead the League of Shadows temporarily, until the Black mask is found. The Black Mask, who escaped Wayne tower before its destruction is now scarred from the explosion with the Mask now seared to his skull. And through the attack on Wayne Enterprises discovered who the Batman is and pieces together his ties to the League of shadows. The battle wipes out most of the League of shadows warriors as well as the false face society and has paid a heavy toll on the city of Gotham.
The climax: Would be Black mask Attempting to assassinate Batman however Talia ends up stepping in front of bullet meant for Batman as her heart has changed after she has witnessed all the destruction caused by her own fathers hand and that of their followers.
Amidst the Chaos created by the battle between the two factions Joker and Harley Quinn escape with their whereabouts unknown to Batman.
By the end of the movie the citizens of Gotham realize that Batman is the only one who can level the playing field against the powers of the criminally insane and the corrupt powers that be in Gotham City. Batman realizes in order to finally win the battle for Gotham City he will need more help than that of the Gotham City Police Department and Commissioner Gordon.