Ned knows this back then so keeps the secret making up the rape story and thinking Rhaegar is the father years later he learns the truth but realizes he can never prove it so declares for Stannis.
Robert and Lyanna appeared to have a political betrothal. It’s doubtful that they ever coupled before she ran off with Rhaegar. Targaryen children tend to look alike due to all of the inbreeding between brothers/sisters. Jon’s dark hair comes from his Stark heritage through his mother, Lyanna.
Although the timeline is not entirely clear, it appears that Lyanna was a “captive” for about year before giving birth.
Many things happened at the Harrenhall Tourney. Legend isn’t necessarily fact.
I’m pissed we weren’t shown the first meeting between Varys and Danaerys, though I did cheer during the shot showing him standing behind her.
“Think it through, Lyanna and Robert could have coupled before the abduction.”
They didn’t, but even if we assume they could have, the war lasted over a year, and the abduction was right at the beginning of the war. So there is no way any progeny of a coupling before the war would be a newborn baby at the end of the war. Never heard of a 12 month pregnancy even in Westeros.