If you are implying that Jon Snow is the son of Robert and Lyanna, then that would not make sense based on last night’s episode. Robert would have no reason to kill his own child by Lyanna, whom he loved, and Rhaegar’s Kingsguard would have no reason to be guarding the Tower of Joy.
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.