After the Tragedy of Summerhall that killed his father and Duncan the Tall, Jaehaerys ascended the throne at the age of thirty-four. Despite his young age, his reign would be short, lasting only three years. Dalbridge, who would later join the Night's Watch, served as a squire to Jaehaerys II in his youth.
The most notable event that occured in his reign was the War of the Ninepenny Kings. The conflict had been brewing for some time. The Band of Nine seized the Stepstones and Jaehaerys feared they would use the islands as a base of operation to launch a war on the Seven Kingdoms. Despite being the least martial of Aegon V's sons, he proved capable of defending realm from the Blackfyre pretender Maelys the Monstrous, the major plotter of the fifth and last Blackfyre Rebellion. Wanting to end the Blackfyre threat once and for all, Jaehaerys assembled the armies of the Iron Throne. Jaehaerys wanted to command the attack against Maelys himself, but his Hand of the King, Lord Ormund Baratheon, counselled the king to remain at King's Landing with Queen Shaera. Instead, Lord Ormund led the attack himself. In 260 AC, the Targaryen armies landed on three of the Stepstones and the war lasted for most of that year. In the end, it was a young knight, Ser Barristan Selmy, who slew Maelys in single combat. With Maelys dead, the rest of the Band of Nine lost interest in Westeros and fell back to their own domains.
Due to his delicate health, Jaehaerys was considered weak by many, but Ser Barristan Selmy, whom he raised to the Kingsguard, thought differently. Jaehaerys's reign only lasted three years, but he reigned well in those short years. He proved a capable king, restoring order to the kingdom, ending the Blackfyre threat and reconciling many of the Great Houses who had grown unhappy with his fathers' reign. In 262 AC, after barely three years on the throne, King Jaehaerys II Targaryen died after a short illness, complaining of a sudden shortness of breath, at the age of thirty-seven.
- Unlike other Targaryen kings, Jaehaerys II was completely omitted from the lore of TV series continuty, making Aerys II the son of Aegon V instead of his grandson.