re: Crackpot ASOIAF Theories SPOILERS

The whole war was started by Rheagar "kidnapping" Lyanna Stark. The end of the war was when Ned Stark and his friends defeated the Kingsguard guarding The Tower of Joy in Dorne where Lyanna Stark was being kept. She was found alive in a pool of her own blood but died after saying "promise me, Ned"

The theory is that she wasn't "kidnapped", she eloped with Rheagar rather than marry Robert Baratheon. Robert, to save his pride, said she was kidnapped and demanded she be returned. Rheagar's dad, King Aegon started burning people alive, including Ned's father, and the war was on.

Rheagar inpregnates Lyana then dies a few months later on the Trident. The Lannisters betray Aegon and sack King's Landing, then Ned takes out the Kingsguard at the Tower of Joy. There, Jon is born of Lyanna, but she dies before Ned can bring her North. To save her legacy, Ned raises the child as his own bastard rather than tell his best friend that his fiance didn't really love him and got preggers by his most hated enemy.