As is suggested in the text, Rhaegar planned some great meeting at the Tourney Of Harrenhal with all the Great Houses in attendance because of Aerys's erratic behavior. Varys gets wind of it and tells Aerys who decides to attend. I believe Aerys attends, blows up Rhaegar's plans to have a council of Great Lords and then informs him about his suspicions about other conspiracies by some Great Lords and how he needs Rhaegar to help him put them down. Aerys becomes suspicious of the Knight of the Laughing Tree and commands Rhaegar to find the mystery knight, but Rhaegar only finds the armor. Many suspect that Rhaegar deduces that it was Lyanna.
Now I'm a believer or more of a questioner of the actions of Rickard Stark prior to the Tourney. Understanding that most Great Lords tend to marry and foster their children to their bannermen to strengthen their loyalties, a Lord that looks outward for marriages and fostering is seen as ambitious. Like Lady Dustin mentions, Rickard had been very busy. Rickard Stark had betroved his heir to the eldest daughter of the Lord of the Riverlands. He fostered his second son at the Eyrie, building ties with his other southern neighbor in the Vale. With the betroval of his eldest daughter to Robert, the Lord of the Stormlands and Lysa Tully bethroved to Jaime Lannister, Rickard Stark would be in a powerful position with strong ties between 5 of the 7 Kingdoms. Imagine how abducting and holding his daughter hostage could keep Rickard in check, in case he had any treasonous ideas. Also this would be a way to draw Rickard out from the North, since invading through Moat Cailin was a non-starter, much less if the Vale, Westerlands and Riverlands sided with the North.
I believe Aerys becomes suspicious of the Knight of Laughing Tree, of course a sign of the North and that's why he sends Rhaegar after the mystery knight. I also believe Rhaegar falls in love with Lyanna and/or sees her as the fulfillment of the PtwP prophecy after he abducts her, they fall for each other at the Tower of Joy and Jon Snow is conceived. But at first he crowns Lyanna Queen of Love and Beauty to let her know, he knows she was the mystery knight and the true champion of the Tourney.
Now when Brandon delivers himself, Elbert Arryn the heir to the Vale and the heirs to Tully bannermen to the Red Keep demanding to kill Rhaegar, Aerys has his chance to punish the conspirators. He arrest all of them and gets Rickard, probably the chief conspirator, to come answer for his treason. After executing the Starks, he calls for the heads of Ned and Robert Baratheon. Since they were both attendees at the Tourney at Harrenhal, Aerys had reason to believe they were in on the conspiracy. Benjen, I believe was too young to be implicate, plus it would allow a Stark to remain in Winterfell who is too young to rebel. Aerys has Jaime as his hostage in the Kingsguard to keep Tywin in check. I think its worth noting that neither Hoster, Catelyn nor Edmure Tully were at the Tourney eventhough it was in the Riverlands and may have suggested to Aerys that they were just unwitting participants in a normal favorable marriage for a 1st daughter of a Great Lord. Jon Arryn could prove his loyalty by delivering Robert and Ned's heads.
Now this theory is to resolve a few nagging questions about Lyanna's abduction, primarily how insane an act it was for the Prince to abduct the daughter of a Great Lord who is promised to another Great Lord, just because he was infatuated with her. Or why Lyanna would run off with Rhaegar when she was bethroved to Robert. But if you look at it as a master stroke by Aerys to blow up the treasonous conspiracy of the Stark/Arryn/Baratheon/Tully/Lannister alliance, where Rhaegar was following orders and they don't fall in love until after the abduction, everyone's actions make more sense. That's why Aerys would back Rhaegar when Brandon comes looking for Lyanna, because Rhaegar wasn't acting alone. And thats why Aerys doesn't send for Rhaegar before the Battle of the Trident. It was because Aerys ordered Rhaegar to abduct and hold Lyanna hostage to break a conspiracy started by Rickard Stark, which Rhaegar might have opened himself up to at the Tourney of Harrenhal, if Varys hadn't uncovered it and warned Aerys.
This I think is especially GRRMish, as from the beginning we've been told that Aerys was mad and evil while the Starks were good and honorable when it would be brilliant if it was the Starks who started the rebellion, proving the unreliabilty of character POVs and how the victors write the history of wars.
Thoughts?
