As leader of the ironborn, he staged two rebellions against the Iron Throne; an unsuccessful one a few years after Robert's Rebellion, about twelve years before the book Game of Thrones begins, a an on-going one that started during the War of the Five Kings. It was in the course of this latest rebellion that Theon Greyjoy, ignoring the orders of his father to raid the Stoney Shore, took it upon himself to seize Winterfell.
In A Feast for Crows, he is killed when during a storm he is swept by a wave from one of the bridges that connect the towers of Castle Pyke. Asha Greyjoy believes that her father was murdered by his brother, Euron. The fact that Euron returned from his years away the day after Balon died, just in time to make a claim for the throne, was too great a coincidence for her.