Ok, it's confusing. The red Zodangans are fighting the blue Heliumites, (the better of the two - because they are "greener" and make life easier for postmen), while being watched by The Tharks (the aliens), who I think we are supposed to like ... but they beat up dogs and one of their women, so it's pretty difficult to care too much what happens to them.
John Carter watches a spaceship battle with his new buddies, the Tharks, but when he sees that Princess Dejah Thoris about to fall, he does his impossibly ridiculous jump (which can have absolutely nothing to do with a slightly different gravity pull on Mars, it is just ridiculous) and snatches her from the air.
Tars Tarkas, leader of the Tharks, gives Dejah to him as his prize. They get talking, and Dejah is sceptical but thinks he may be a messenger from the Gods. With the help of Sola (the Thark girl who is constantly punished) and Tarkas to escape (who turns out to be Sola's father), she leads him to a mystical place called Isis. They find a giant pyramid, which turns out to be powered by this "9th ray" that Dejah almost discovered in her Science Fair experiment before. Carter's medallion turns on a few lights, and they can see the solar system inside the sanctuary. Carter finds out that we've all been a bit stupid, and should be calling our planets words that rhyme with "Baboom".
Outside, one of the Therns (disguised as a Thark), has managed to turn a whole Thark clan against them and they give chase. Carter does his best to defeat as many of them as he can, until they are saved by a few airships ... and it seems that the civil war has ended. Sab Than, the bad guy, tries his best to win over Dejah. They take Carter back to Zodanga.
Carter soon escapes with the help of one of the Princess's men and finds Dejah in her wedding dress. She guesses they'll never be together when he sees that he is still wearing his own wedding ring. He hides when her aides return for her...
But not before the old Grandma re-enters the room, turns out to be Mark Strong the head-honcho Thern, who zaps him ... and then forces JC to tag along and listen to his boring story about Mars. JC luckily manages to escape when his dog dives on the scene and disrupts the Thern's blu-ray.
Carter escapes on a pod-racer (looks familiar) and races over to the Thark Separatist city (sure I've seen this before). Tarkas has been deposed by the Thark with one tusk, and they are forced to fight as Gladiators in an alien colosseum against giant beasts (this deja vu is getting creepy now...). Carter defeats two giant gorilla-beasts, then challenges the one-tusk alien, lobs off his head, and now takes charge of the Tharks. If only life was this simple.
Carter jumps onto his spaceship and heads over to Zodanga to stop the wedding ... but geography was never his strong point and the city is empty - the wedding is in Helium. Sab and his boys probably thought it would be a good party trick if the Best Man spoke with a high-pitched voice during his speech.
Carter crashes the party. The wedding is ruined, so the Zodangan's start a riot outside. Things are not going too well for the Heliumites until a huge spaceship crash lands and the Tharks join the fight. Sab is defeated, and Carter does the honorable thing and makes an honest woman out of Dejah.
That night he goes for some fresh air when Mark Strong appears to spoil the party and Carter is teleported back to Earth, where he wakes up looking like Rip Van Winkle.
Carter threw away his medallion and cannot return, so we continue from the beginning of the movie where he has spent his life trying to hunt down for a medallion on earth so he can get out of here and enjoy some nookie with Dejah. Of course, if she liked him she should also be trying to do the same and at least she'll know there's a few medallions knocking about on random people's necks, but she just isn't as committed it seems.
Carter's nephew is a quick reader and has finished the novel in one sitting. He is warned to protect the body, so he races out to the crypt, guesses the password and enters ... only to be followed by one of those nasty Therns. Carter shows up and guns him down, and scares the life out of his little nephew.
He takes the Thern's medallion, and asks his nephew to protect his body. He enters the crypt, lies down, and repeats the phrase to go home ...
So, after the credits, Carter teleports back to Mars ... only to find that Dejah, in her loneliness, decided to claim on his life insurance and marry Tars Tarkas instead. (Just kidding).