On Barsoon, John is able to leap incredibly high and far because of its weaker gravity, and he is stronger because of his higher bone density. When he gets there he is at first unable to understand the aliens, but eventually he is able to.
In the mid 1800's in the Arizona Territory, John Carter is prospecting for gold and having violent encounters with the local Apache Indians. After he was captured by Colonel Powell, who wishes to Shang-high Carter back into active military service. Carter tries to escape from imprisonment. John goes on horseback to escape and the accidentally runs into a group of apaches. When one of the apaches is accidentally shot, a fight breaks out.
Powell gets hurt, John goes back for Powell and the pair take shelter in a nearby cave, John discovers a large quantity of gold. A strange figure suddenly materializes in the cave; John kills his would-be attacker and, due somehow to the stranger's large elaborate medallion, is inadvertently teleported to Barsoom (Mars). There, due to his different bone density and the planet's lower gravity, John is able to jump fantastically high and throw killer punches. He is soon captured, by the giant, four-armed Green Martian Tharks under the rule of Tars Tarkas.
Elsewhere on Barsoom, the cities of Helium and Zodanga have been at war for a thousand years. The Jeddak of Zodanga, Sab Than, is now armed with a special weapon given him by the Therns, and proposes a cease-fire and an end to the war by marrying the Princess of Helium, Dejah Thoris. The defiant Princess escapes and is rescued by John.
John, Dejah, and Tarkas's secret daughter Sola embark on a quest descending the sacred River Iss to find a way for Carter to get back home. There they find information about the medallion, and the process by which the Therns teleport ("telegraph") from planet to planet, but they are attacked by the Thern leader Matai Shang and his minions, the Green Martians of Warhoon.
After the attack, Carter is captured and taken back with Dejah, while Sola is able to escape. Dejah agrees to marry Sab Than, then gives Carter his medallion and tells him to go back to "Jasoom" (Earth). Carter decides to stay back and is now captured by the shape-shifting Matai Shang, who tells him about the secret purposes of the god-like Therns and their age-old manipulations of the histories of civilizations on different planets. John is able to make yet another escape thanks to the faithful Martian hound Woola, and he and Sola go back to the Tharks and ask for their help.
There they come to know that Tarkas has been overthrown as Jeddak by the vicious Tal Hajus. Tarkas, Carter, and Sola are subjected to a gladiatorial contest with two gigantic white Martian apes. After defeating them and killing Hajus, Carter is acclaimed leader of the Tharks. A vast Thark army, with Carter at its head, advances on Zodanga, then on Helium, and defeats the Zodangian army, killing Sab Than. Carter then marries Dejah himself and becomes Jeddak of Helium. That night, Carter decides to stay forever on Mars and throws away his medallion. Seizing this opportunity, Shang re-emerges from hiding and banishes him back to the Earth.
Resuming the original framing story, it is revealed that Carter has undertaken a ten year long quest, looking for clues of the Therns' presence on Earth and hoping to find another medallion. His sudden "death" and unusual funeral arrangements would seem to indicate that he has succeeded and returned to Barsoom, leaving his "Earth body" in a coma-like state. His presence on Mars was via a sort of virtual body, and the death of his Earth body would end his life on both planets. He makes Ned his protector, giving him clues about how to open the mausoleum. Ned now hastens to the mausoleum, opens it, but finds no body. He has been covertly stalked by Shang, in the form of a man with a bowler hat. As the would-be assassin prepares to strike, Carter suddenly reappears and kills him. He discloses to Ned that he never found any medallion, but instead laid a clever trap for a Thern to get that Thern's medallion. John then takes Shang's medallion, invokes the necessary code words, and is instantly teleported back to Mars, to continue his Barsoomian life with Dejah.
- John Carter was not married in the original novel, in the film he had a wife and daughter before they were killed by known assailants. Furthermore, in the novel, he reveals that he is immortal and thousands of years old. The movie does not mention this, though it could be implied.