Mal was born on September 20, 2486 and was brought up on a ranch on the planet Shadow. Raised by his mother and "about 40 hands", Mal apparently received fairly decent education growing up. Though Mal usually seems more practical than intellectual, he occasionally surprises his friends by displaying familiarity in a wide range of literature varying from the works of Shan Yu (a fictional psychotic dictator) to poems by Samuel Taylor Coleridge.

Mal volunteered for the Independents army during the Unification War against the Alliance, gaining the rank of sergeant during that time. His loyal second-in-command Zoë was by his side for most of the war, surviving many dangerous conflicts with him. The show mentions three such battles, including the Battle of Du-Khang in 2510 (featured in "The Message") and a long winter campaign in New Kashmir (as told by Zoë in "War Stories") where he commanded a platoon. Mal was also involved in the ground campaign during the Battle of Sturges (Serenity (the comic book) #2), which according to Badger was the "bloodiest and shortest battle in all the war", although Mal considers it a distant second. Mal fought in many more battles, but the turning point for him and the Independents came with their physical and emotional defeat at the Battle of Serenity Valley on the planet Hera. On-screen information from the film Serenity suggests that Mal was given a brevet promotion to Captain during the Battle of Serenity Valley to take command of the ever-increasing number of Independent troops who were losing their officers at the hands of the Alliance. This might explain why, in one of the deleted scenes from the Firefly pilot, Mal is described as having commanded at least 2000 men. On-screen information in Serenity shows him to have been attached to the 57th Brigade; in the series pilot, Badger calls it the "Balls and Bayonets Brigade", though it is unclear whether that was a disparaging nickname coined by Badger himself or the actual unit sobriquet.

After the war, Mal acquired his own ship, an old (broken) 03-K64 Firefly-class transport whose previous owner was a man named Captain Harbatkin (and he never got around to changing the registration papers). He promptly named the ship Serenity. On board Serenity and during his various travels, Mal continues to wear his brown coat and wields a standard issue officer's pistol as his weapon of choice, a gun which he has had since the war and which he has modified extensively.

It seems that the war, and particularly the Battle of Serenity Valley destroys Mal's religious beliefs. In the opening of the series pilot, he speaks of God when rallying his troops, and kisses a cross hanging from his neck before going into battle during the Battle of Serenity Valley. Later, however, he is uncomfortable having Shepherd Book on his ship, and the two characters' difference of opinion on the matter of religion is a constant source of (usually friendly) conflict. (Mal tells Book shortly after he arrives on board Serenity, "You're welcome on my boat. God ain't.")

Mal's crisis of faith is elaborated further in a deleted scene from the pilot episode, which gives more detail on the losses in the battle. After the Battle of Serenity Valley, both sides leave the survivors without medical attention for a week while negotiating the truce. Over half of them die of their wounds or disease (similar to the immediate aftermath of the American Civil War battle of Cold Harbour). When medical ships finally arrive, his response to Zoë's utterance of "Thank God," is "God? What colour’s he flyin'?"

Though Mal loses faith in God and religion, he retains a strong faith in humanity. Though wary in his personal dealings, he puts great stock in the fundamental goodness of people in general. This faith in individuals' abilities to do the right thing manifests strongly in his very negative view of governmental institutions. "Governments," he says in the pilot, are for "getting in a man's way." The Alliance, whose government seems particularly fond of interference and regulation, is thus his logical nemesis. His contempt for the Alliance never completely disappears and, although he was on the losing side of the Unification War, years later he still isn't sure it was the wrong one. In Serenity (film), Mal expresses what seems to be his manifesto - "[The Alliance] will swing back to the belief that they can make people... better. And I do not hold to that. I aim to misbehave." His anti-government attitude is reflected in his choice to live on a spaceship, drifting from world to world, as far away from Alliance interference as possible.

The ship is a means of escaping the loss of the war and the resulting Alliance dominance over the systems, and the show focuses on Mal's attempts to get by in a Universe that that has forsaken him. He takes whatever jobs he can get turning a blind eye, if he can, to the legality of the job, but never doing the wrong thing in terms of morality. He is a man of compassion (refusing jobs that would involve him in slavery, for instance), with a strong sense of nobility. He is, however an anti-hero and will kill those who threaten him with a philosophy that, "If someone tries to kill you, you try and kill them back." He is not above joking with his crew or picking bar fights, but he retains his honour in the face of adversity. What separates him from typical heroes is that Mal is the kind of guy who is willing to shoot first and skip the question. He is not above petty theft but often rationalizes such behaviour to make it appear more noble or valiant (such as stealing from Slavers).

He is very protective of his crew and fiercely loyal. He retains the idea that you never leave someone behind and, once you are a part of his crew, you are assured his protection. He treats an attack on a member of his crew as being tantamount to a direct assault on him and will not stand for it. He is also a natural leader, inspiring loyalty that is reciprocated as is shown in both his war experiences and in his relationship to his crew. It is hinted throughout the series that Mal and Inara Serra, a courtesan or Companion, have strong feelings for one another. Both seem to be trying to hide their true feelings, however, and can seem to only release the tension by quarrelling most of the time.

He is commonly called Mal in the show but he is also called "Captain Tightpants" by Kaylee in the episode "Shindig" and this name has become popular with the fans of the show.