After reading and listening to the available books and audiobooks over 15 times or more by now, I believe Jon Snow is the legitimate son of Rhaegar Targaryen and Lyanna Stark. Rhaegar was married to Elia Martel. They had two children, Aegon Targaryen and his sister Rheanys Targaryen. After the birth of Rheanys, Rhaegar was told by the maesters that Elia can no longer bear another child as it will kill her. According to Daenerys Targaryen vision in the house of the undying, Rhaegar was seen and heard taking to Elia Martel saying “The Dragon must have 3 heads”. To make a long story short, Rhaegar married Lyanna Stark as a second wife just like Aegon the Conquer married his two sisters. Elia out of duty and Lyanna out of love. From the union of Rhaegar and Lyanna comes who we know as Jon Snow. I Believe Jon’s real name will be Amon Targaryen after Maester Amon which Rhaegar had a close relationship with especially concerning the prophecy of Ice and Fire and Maester Amon was named after Amon Targaryen the Dragon Knight. Jon Snow shows a lot of the same personal characteristics of Amon the Dragon Knight when you go back and re read what little passages there are about him. Jon Is the third head of the Dragon, half brother to Aegon the VI and nephew to Daenerys Targaryen. When Eddard Stark found his sister Lyanna in the Tower of Joy, Lyanna made Eddard promise her something. If Jon is truly the son of Rhaegar Targaryen, his life would be in danger if Robert Baratheon ever found out. Robert’s hatred of Rhaegar out weighs his love for Lyanna and so Jon must die if his identity was known. Just like the other Dragon Spawn. Not to forget, Ser Arthur Dane “The Sword of the Morning” Rhaegar Targaryens closest friend after Jon Connington. Ser Gerald Hightower the Lord Commander of the Kings Guard was also guarding the Lyanna Stark and her newborn child. Why else would the Commander of the Kings Guard sit and protect Lyanna Stark and her child if they were not part of the royal family at this point? The Lord Commander stays with the King or Prince in times of trouble.
Jon Snow’s personality parallels that of Rhaegar’s and Amon the Dragon Knight as the story progresses. The only thing missing is someone telling Jon how much he is like Rhaegar in the same way Daenerys has Ser Jorah Mormont and Ser Bartistan Selmy tell her. So now the story as we wait for book 6 has the 3 Dragon heads and the Prince and Princess that was promised. It may still be possible that Aegon the VI may be an imposter. The warning Quaithe gave Daenerys, “Beware the Mummers Dragon” a direct reference to Aegon the VI as far as know.
