So. Many. Fan theories.
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Tower of Joy
Approximately a year after the Tourney of Harrenhal, Prince Rhaegar kidnapped Lyanna Stark and imprisoned her in a remote tower. Or Lyanna Stark ran away with her lover Prince Rhaegar to give birth to their child. While the latter is 99.99% the most likely scenario, Lyanna’s betrothed — Robert Baratheon — was unable to accept this reality. Instead, he convinced himself of Rhaegar’s evil intentions and declared open war on the Crown Prince.
The only two people alive today who know for sure what happened at the Tower of Joy (ToJ) are Barristan Selmy and Howland Reed…because the rest (save Ned Stark) died in battle over Lyanna at said tower. But why would the Kingsguard die to protect her? Because, based on context clues, Lyanna Stark is most likely the mother of Jon Snow…with Rhaegar Targaryen being his father. With Robert on the warpath — murdering all potential Targaryen offspring, illegitimate or otherwise — Lyanna made Ned promise to keep her infant boy safe while dying in childbirth (or after the heat of battle if she donned her armor to defend the ToJ from her brother and his cohorts).
Art by: Henning Ludvigsen