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What is the story behind Rhaegar and Lyanna?

I remember reading in one of the books that Rhaegar won the tourney at Harrenhal and named Lyanna Stark the Queen of Love and Beauty. And there's also a mention elsewhere where Robert Baratheon says "if Rhaegar hadn't laid eyes on Lyanna, she would have been alive".

Was Rhaegar responsible for Lyanna's death/suffering directly or indirectly?

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If you've read the books, perhaps you will recall the story of The Knight of the Laughing Tree, which Jojen and Meera Reed told to Bran? That's the story of that tournament, and there are many clues and things half said there which are interesting to read. – TLP Dec 19 '13 at 12:58
Yes, I remember bits of it. But they don't tell the whole story. I wanted to find out what other clues there are, scattered in the books. Thanks for the link! – Aswath Dec 19 '13 at 13:00
up vote 16 down vote accepted

Clues about Rhaegar and Lyanna, together, or by themselves:

Rhaegar is (presumably) mentioned in Daenerys' perspective, in the House of the Undying prophecies (also here) like this:

Rubies flew like drops of blood from the chest of a dying prince, and he sank to his knees in the water and with his last breath murmured a woman's name.

Presumably this woman is Lyanna. Also noted in the prophecies is:

A blue flower grew from a chink in a wall of ice, and filled the air with sweetness.

Which may be a reference to Jon (at the Wall), the presumed love child of Lyanna (blue roses) and Rhaegar (link to Daenerys).

And of course, Daenerys sees Rhaegar as one of the visions in one of the rooms in the House of the Undying:

The man had her brother’s hair, but he was taller, and his eyes were a dark indigo rather than lilac. "Aegon," he said to a woman nursing a newborn babe in a great wooden bed. "What better name for a king?"

"Will you make a song for him?" the woman asked.

"He has a song," the man replied. "He is the prince that was promised, and his is the song of ice and fire." He looked up when he said it and his eyes met Dany, and it seemed as if he saw her standing there beyond the door. "There must be one more," he said, though whether he was speaking to her or the woman in bed she could not say. "The dragon has three heads."

The woman would be his wife, Elia of Dorne. Presumably, the "third head" he is talking about is Lyanna.

The prohecy Rhaegar is referring to there is the one foretold about the Prince that was Promised, which was retold to Rhaegar's great grandfather Aegon V Targaryen (aka Egg from the Dunk & Egg novels) by the Ghost of High Heart (the little dwarf ghost lady that Arya meets when she travels with Lord Beric's gang). She foretold that The Prince that was Promised should come from the line of the mad king Aerys II, which is something that Rhaegar took to heart. Aegon V's daughter is also coincidentally Robert Baratheon's grandmother.

The propecy of the Ghost of High Heart eventually lead to the Tragedy at Summerhall, the Targaryen summer residence which was the seat of Maekar, the father of Aegon V (Egg). The tragedy was presumably the result of an experiment to hatch dragons by Aegon V. Prince Rhaegar was born on the day of that tragedy, and may be the "dragon" that was hatched. Rhaegar was often preoccupied with this tragedy, spending time alone in Summerhall and writing sad songs.

In the story of the Knight of the Laughing Tree, we see Rhaegar at the tournament at Harrenhal, where he crowns Lyanna the Queen of love and beauty. A theory about this event is that Lyanna is the mystery knight, and that Rhaegar unmasked her, therefore thinking of her as a great warrior maiden (which she by accounts was). Which may be why he crowned her, and why he felt she would be a suitable "third head" in his prophecies.

All in all, Rhaegar was a melancholy man that was preoccupied with prophecies. It does not seem likely that he would abduct and rape a woman, like Robert claimed.

Also, of course, we have the promise that Ned Stark made to Lyanna (Promise me, Ned -- AGOT), when she was in her death bed. What could it possibly have been, that Ned would obsess over it during his time in King's Landing and in the dungeons? A good guess would be something to keep secret from Robert, because Robert swore to "kill all the dragonspawn [he] could get [his] hands on", such as a son of Rhaegar: Jon.

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+ 1000! @Aswath you should accept this answer instead. – System Down Dec 19 '13 at 17:14
I totally forgot about Daenerys' visions about Rhaegar. Thanks TLP! – Aswath Dec 19 '13 at 18:27
@SystemDown Thank you. Aswath: You're welcome. – TLP Dec 19 '13 at 18:29
Huh, I'd never put it together than Jon might be Rhaegar's son. Interesting hypothesis and lots of evidence to back it up. Great post. – Andrew Bartel Dec 21 '13 at 20:12
@AndrewBartel This is not really meant to show the clues to Jon's parentage, there are better expositions on that topic. Google "R+L=J" and you will find a myriad of threads on that. – TLP Dec 21 '13 at 23:53

Here be spoilers:

Known Facts:
At the time of the famed tourney of Harrenhall, Lyanna Stark was betrothed to Ned's best friend Lord Robert Baratheon, while Prince Rhaegar Targaryen was married to Princess Elia of Dorne. Rhaegar eventually won the tourney and the right to name the tourney's queen of love and beauty. Tradition required him to name his wife to the title, but instead he gave the title to Lyanna Stark causing a great scandal. Sometime later Lyanna is spirited away by Rhaegar, an event that would eventually spark the Baratheon/Stark rebellion against the Targaryens.

Robert Baratheon's version of the story:
Rhaegar kidnapped and raped Lyanna repeatedly, and imprisoned her in a tower called the Tower of Joy. She eventually died from wounds sustained during her captivity.

Rumors and hints to the real story:
- It is heavily hinted by several characters that Rhaegar and Lyanna shared a mutual attraction, and that the two of them eventually eloped.
- Being a Targaryen, it was not unheard of for Rhaegar to take a second wife. This hints that the two may have married in secret.
- The Tower of Joy was not Lyanna's prison but a protected sanctuary, as evidenced by having no less than three of the seven Kingsguard manning it.
- Ned describes his sister dying in a bed of blood. Since no violence was inflicted upon her this hints at death from birth complications.
- A popular theory states that the child Lyanna gave birth to was Jon Snow. Lyanna extracted a promise from he brother to protect the child, so Ned claimed him as his own bastard (besmirching his own honor) to hide his identity.

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If Rhaegar would have had a legitimate male child, would he stand to inherit the throne? – Martin Epsz Dec 19 '13 at 14:30
Not while Robert Baratheon could still wield a war-hammer... but he would have a strong claim now, yes. – TheMathemagician Dec 19 '13 at 14:51
@MartinEpsz - Any child of Rhaegar would definitely have a claim to the Iron Throne. In fact, this hypothetical (or not) son's claim would be stronger than Daenerys's. – System Down Dec 19 '13 at 17:12

Massive spoilers here, fairly obviously.

The Rhaegar/Lyanna situation was the cause of Robert's Rebellion and the overthrow of the Targaryens, so it was a pretty major event. The Baratheon/Stark version of events is that Rhaegar abducted and raped Lyanna, and she died of her injuries before Ned could get to the Tower of Joy to rescue her after Rhaegar's death at the Battle of the Trident. However, reading between the lines, it seems more likely that Lyanna (a wild child) eloped with Rhaegar of her own free will, possibly married him in secret (there's precedent for Targaryens being allowed more than one spouse), and died giving birth to his child, who is Jon Snow.

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So who was Rhaegar already married to, when Lyanna eloped with him? – Aswath Dec 19 '13 at 7:54
Princess Elia of Dorne. Her death at the hands of Robert's forces is the reason why the Martells of Dorne are now hatching their own plots for the future of Westeros. – Mike Scott Dec 19 '13 at 8:16

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