Official Canon Edit
Jaghatai Khan was found on Chogoris, a feudal world where most people lived nomadically on horseback. After he united his people, he was found by the Emperor and was reunited with his legion, the White Scars. In order to keep new recruits battle-hardened, Jaghatai dissolved his empire and allowed the various tribes to fight each other once more.
Over time, the Khan saw himself as an outsider, and found it difficult to get along with most of the Imperial citizens, including his brothers. However, he formed a close bond with Magnus the Red, who shared in his outsider status, and both loved to take up intellectual pursuits. While Magnus was always fascinated by the Warp, Jaghatai encouraged him to exercise more caution, and not to draw out more power than he needed. Unfortunately, his words went unheeded when, after the council of Nikea, Magnus continued to look into the Warp, and became a pawn of Tzeentch.
Horus Heresy Edit
Upon learning of the fate of Prospero, Jaghatai went to investigate. There he encountered a shade of Magnus, who relayed what had happened. Jaghatai escorted the remaining loyalist Thousand Sons away from the planet, just as Mortarion and his Death Guard arrived. Khan refused Mortarion's offer to join Chaos, and defeated him in a duel. Khan made for Terra, where he assisted the Imperial Fists in defending the planet from the Traitors.
After failing to protect the Emperor, Jaghatai Khan disappeared into the Webway to rescue Imperials from the Dark Eldar.
TTS Canon Edit
Jaghatai Khan was a speed demon who could not hold still for more than a second. Custodisi spotted him surfing a Rhino during the Seige of Terra, and reported that the real reason he disappeared into the Webway was to challenge the Dark Eldar to a race.