Batman: Ra's Al Ghul
While the Joker had no reasoning to his villainous acts, Ra's al Ghul had plenty of reasons for his acts as he justified them with the fact that humanity was flawed. His name literally translates to Demon's Head or the Head of the Demon. He thought it was best to rid the world of humans as they simply destroy. Ra's al Ghul in a dysfunctional kind of way almost serves as Bruce Wayne's father. The two had a father and son relationship where they loved each other and hated each other all at once. Ra's saw Bruce as his future son and tried to seal the deal by having him marry his daughter Talia which would then have him become the future leader of the League of Shadows. The League of Shadows was a group of assassins led by Ra's and while he knew his time would eventually end, he wanted to make sure he had his successor. Ra's has lived a long time thanks to his magical Lazarus Pit which helped defy the odds and essentially become immortal. He was a great villain because he was not exactly a madman but he was more a radical realist as he knew what humanity was capable of. Even more so, he knew Bruce's mind inside and out more than most other villains.
Ra's was born over six hundred years ago to a tribe of nomads somewhere in the deserts of Arabia. He was interested in science at a very young age and since he was unable to increase his knowledge within the tribe he left them to live in a city where he could learn more. He would go on to become a psychian where he would meet the love of his life in the form of a woman named Sora. Ra's also discovered the secrets of the Lazarus Pit when he lowered a dying prince into it, when the prince emerged full of life he then realized the power it held. However, the prince was sadistic already, and when risen out of the pit he was even more insane. The pit would grant near immortality but came at a price of the users sanity. The prince would eventually go on to take the life of poor Sora. The prince then turned his attention to Ra's and declared him guilty of the crime and sentenced him to a slow death, tortured death in a cage with the corpse of his beloved Sora. He would eventually be freed by the son of an elderly blind woman, despite Ra's inability to save her from an untimely death. The son of the woman felt that he had owed Ra's for his attempt to at least ease his mother into her death and making it the least bit traumatic for her. Upon his escape, the boy and Ra's head to the tribe that he was born into asking for their help to take down the prince in a fit of vengeance. He also had wanted to ensure the downfall of the king of the city. Due to Ra's advanced intelligence in science, he developed a virus that infected the prince by sending him contaminated fabrics. When the prince is finally knocking on the doorstep of death, the king of the city visits Ra's with his son asking for a cure only to be killed by Ra's. He then led his tribe into the city where he killed all of it's inhabitants and declared himself "Demon Head." Ra's spent the next several centuries journeying across the world while he, his uncle, and the boy who saved him continuously used the Lazarus Pit. Ra's eventually killed the boy when he found out that he had been taking records of their endeavors, and upon finding this out the uncle took off with the memoirs that the boy wrote. In his solitude, he found the time to master many different forms of combat and taking a likening to fencing. In this time he also built up a vast amount of wealth and created a international organization called The Demon, which was also apart of his League of Assassins.
Ra's appeared in Gotham in the story line called "Contagion" where he came dangerously close to realizing his dream of worldwide genocide. He did so thanks to his organization's help as they unleashed a deadly virus called Ebola Gulf in Gotham which effectively put Batman in conflict with a force he would have a hard time triumphing over. As always, Batman and his allies would find a cure to the virus, although he was unable to get his hands on the elusive Ra's al Ghul until the storyline called "Legacy." In this storyline, Batman and his allies searched around the globe for Ra's while preventing future outbreaks of the virus. To make matters worse, it is later found out that Ra's had allied himself with the villain Bane who had severely hurt the Bat in a brutal fight previously. Ra's looks at Bane as a potential heir to his empire down the line, despite his daughter, Talia's distaste for such a brutal criminal. Over time, a way to eliminate the virus would be find out thanks in large part to the Wheel of Plagues artifact, which aided Ra's in the creation of the virus. After the virus was supplanted, Ra's once again would escape the Bat. However, Ra's did meet his end when he was shot and killed by his long lost daughter Nyssa who was set out on a mission to kill Superman with kryptonite bullets. After getting shot, Ra's revealed to Batman that it was all part of his plan as now he was able to show his daughters the evil that humanity is capable of as he left Nyssa in a concentration camp at a young age. When she left she was so stricken with rage that she had the crazy idea of attempting to kill Superman, which in fact, would then destroy all hope and optimism in the world. Nyssa and Talia then become the heirs to his throne, and Talia disavows her love for Bruce Wayne while the sisters also declare Batman their sworn enemy. Nyssa then stabbed her father straight through the heart to ensure his death, but Batman had him cremated just to be sure he was dead for sure.
Over the years, Talia al Ghul and Bruce Wayne had a son named Damian. One day Talia took her son to the Australian Outback where he was tutored in secret on the history of his grandfather, Ra's al Ghul. Talia is unaware of the fact that a former servant of her father has plans to use Damian as a shell for the soul of Ra's to possess. Upon her realization of this and the fact that the process would kill her son, she saves him at the last minute. However, Ra's is still able to return to our plane of existence as a living corpse, but still needing to possess the body of Damian to stabilize himself. Damian returned home in search of his father to inform him but is met by Robin. He tells Robin what he has seen, only to be surprised that Robin does not believe him. The two engage in a fight where Damian actually bests Robin and knocks him out. Eventually the news hits Batman, to which he takes off to Asia where he saves Talia from a League ninja before setting off to find Ra's. Upon arriving at Ra's headquarters, he is surprised to see that his henchmen had kidnapped both Damian and Robin. Batman attempts to fight Ra's but cannot hurt him as he is already dead. He then offers Batman a choice as to which body to inhabit, Robin or Damian. Batman, the selfless hero that he is, then offers himself, but Ra's says he is too old of a body to withstand the process. Batman then tells Ra's of another option, the Fountain of Essence (yes this is all beginning to sound like something Michael Bay would think of) which is similar to the Lazarus Pit but with none of the dangerous after affects. Upon arriving at the temple that holds the fountain, they are hold off by the Sensei, who happens to be Ra's father much to his surprise. Ra's and Batman make quick work of the Sensei's henchmen but then are quickly thwarted by Sensei. Batman with a broken arm, blinded and impaled was still determined enough to save the day and managed to get one good shot in on Sensei that sent him flying into the Fountain of Life which killed him for not being a pure soul. Ra's possesses the body of one of the monks and walks away while Batman is slightly de-aged and restored to full health. He realizes what Ra's has done and angrily screams for his name. Ra's new body is still not enough to hold him and continuously searches for the perfect match for his soul but eventually is defeated by Batman and thrown into Arkham Asylum.