Golden Age

During the Golden Age, Thomas Wayne played a less lucrative part in Batman's origin other than the fact that his murder propelled Bruce into becoming Batman. He first appeared in Detective Comics #33 November 1939. In the story,Thomas and Martha were exiting a theater when a mugger named Joe Chill stopped them. Thomas tried to protect his wife and son when the Chill shot him. The shock of seeing her husband die gave Martha Wayne a heart attack and she died with him. Years later, Chill would become a racketeer, transporting wanted criminals across the state lines. Batman reveals his identity to Chill accusing him of murdering his parents. Shocked that he was the one responsible for the creation of Batman, Chill ran to his men in the garage. When they find out that Chill is responsible for the creation of the Batman, they shoot him dead.

Silver Age

During the Denny O'Neil-Neal Adams era, Thomas Wayne's character was further developed and tied to Batman's origins. Dr. Thomas Wayne wears a bat themed costume for for a party. When he took first place for the best costume, two gangsters come in and kidnaps him. They take Thomas to their boss Lew Moxon who was shot during a bank heist and wants Thomas to remove the bullet. Thomas knew that if her removed the bullet, Moxon would kill him. So he took the only chance he had and he kicked Moxon's chair and he fell to the ground. He then attacked to two remaining and when the police arrived they found the gangsters lying on the ground out cold.

Lew Moxon was arrested and pout on trial and was convicted ten years in prison in one of Gotham's shortest trials in history. Later, Moxon would resurface and vowed that he would get even with Wayne. So he hired Joe Chill to pretend to be a mugger and kill Thomas and Martha so that young Bruce would testify that his parents were killed by a mugger.

Years later, when Bruce was thinking of becoming a symbol to strike terror into the hearts of criminals a bat flew through his window. Seeing the bat reminded Bruce of his father wearing the bat costume and he designed a similar costume and became the Batman. Batman would eventually find Joe Chill and similar to the earlier stories, Chill was killed by his own men when they realize his role in Batman's creation. As Chill died, Batman say that:" It was not Batman that finished you it was Bruce Wayne". Sometime later, Batman discovers that it was really Lew Moxon who was responsible for his parents murder. Batman tracks Moxon down and it is revealed that Moxon has suffered amnesia due to an accident some time after the Wayne's death. Because Batman's suit was torn during a fight, Robin suggests that he wears his father's bat costume instead. With his father's costume Batman confronts Moxon who runs away frightened onto street where he dies after a truck hits him.

In the Secret Origins of The Batman, Batman says that he may have trained years to become the World's Greatest Detective and hunted down all those super villains but he couldn't find a two bit gun man. Batman also says that he hasn't visited his parents grave ever since he captured Chill but knows they will always be with him in his spirit.

Post Crisis

After the Crisis on Infinite Earths, much of the DC universe was retconned. In the new origin, Bruce fell down a fissure (or a well)that would one day become the Batcave. Thomas rescued his son from the cave but Bruce was already traumatized by the bats in the cave. This happened when Bruce was only four years old. Later when Bruce was eight, his parents take him to see the mark of Zorro when they were returning from the theater a mugger stop them and kills Thomas and his wife. In The Long Halloween it was revealed that crime boss Vincent came to Thomas Wayne to operate on his son Carmine Falcone who had been shot during a gangfight. Thomas wanted to take him to a hospital but Vincent disagreed so he performed the surgery in the dining room. After the surgery, Thomas was offered a reward for saving Carmine Falcone but he refused saying that "to a doctor, a patient is a patient."

Meanwhile, young Bruce watched all this from behind. After it was revealed that Carmine Falcone was behind the holiday killings. Bruce wonders if Gotham was better off if Thomas hadn't saved Falcone's life.

After Death...

In the wake of their murder, Bruce Wayne and Gotham itself was forever changed. Bruce Wayne began to take a darker path in his life and the citizen's of Gotham began to lose faith in it's police department seeing such prominent citizen's die so easily. As a result the police officer's lost faith in themselves. The exact time of the Wayne family murder is 10:47 on June 26th, the Batcave is accessible once the grandfather clock is tuned to this time.

Death and Maidens

In this storyline, Ras Al Ghul offers Batman a chance to talk to his parents. Batman, hesitant at first, swallows an elixir and believes that he is speaking to his parents. Surprisingly though, both his parents disapprove of Bruce's costumed crusade. They both believe that Bruce has sacrificed too much and his chance of happiness by becoming Batman. As they leave, both of them assures him that the lessening of his grief does not mean he (Bruce) no longer cares for them. After his experience Bruce realizes that he is Batman only because he chooses to be not because he has to be.