The Assassination of Jon Arryn was a secret plot orchestrated by Petyr Baelish in an attempt to throw the Seven Kingdoms into a state of chaos from which he could personally benefit. It took place just prior to the events of the series and has far reaching consequences in Westeros.
Following Robert's Rebellion, Jon Arryn was appointed as Hand of the King to King Robert. While Robert devoted his energies to whoring, drinking and hunting, Arryn was effectively left to govern the realm and apparently did so wisely. After seventeen years as Hand, Arryn died suddenly of a fever.
At Winterfell, Eddard Stark learns of Jon Arryn's death and that King Robert and the royal party are bound for Winterfell. Eddard realizes that Robert intends to name him as his new Hand. He considers refusing but Lady Catelyn receives a letter from her sister Lysa, Jon's widow, claiming that her husband was poisoned by the Lannisters. With this news, Eddard is convinced to accept Robert's offer so he can investigate Jon's death.
Once in King's Landing, Eddard starts his investigation. He discovers that just prior to his death, Arryn acquired a book from Grand Maester Pycelle: The Lineages and Histories of the Great Houses of the Seven Kingdoms and visited several of King Robert's bastard offspring. He deduces that Arryn was investigating the parentage of Robert and his wife Cersei's three children. Varys, the Master of Whisperers, warns Eddard that he believes Jon was actually poisoned using tears of Lys, a poison that is rare, costly and difficult to detect. When Eddard inquires as to motive for the murder, Varys simply replies, "He started asking questions".
Tyrion Lannister is apprehended by Lady Catelyn, who accuses him of trying to kill her son Bran. She takes him to the Eyrie, Lysa's home. Once there, Lysa accuses him of orchestrating Jon Arryn's death too. After a trial by combat, Tyrion is acquitted.
Under interrogation from Tyrion Lannister, Grand Maester Pycelle admits that Arryn had discovered that truth about Cersei's children; that they were not fathered by Robert, but by her brother Jaime, and he intended to inform the King. Pycelle also admits that Arryn was poisoned but strongly denies doing it himself. Tyrion nevertheless says Pycelle was complicit and let Arryn die because of the threat he posed to the Crown.
The full truth of Arryn's death is finally revealed by Lysa Arryn in a conversation with her new husband Petyr Baelish. To prove her love for him, she reminds Baelish that, on his instructions, she laced Jon's wine with Tears of Lys and then sent a letter to her sister falsely accusing the Lannisters for this murder.
In the books
In the A Song of Ice and Fire novels, the assassination of Jon Arryn is carried out in the same manner: Tears of Lys on his wine. However, Lysa Arryn is not only motivated by her obsession with Littlefinger but also her refusal to have her son Robin sent off to Dragonstone to be fostered by Stannis Baratheon as Jon Arryn intended. Arryn is treated by Colemon, his maester, but Pycelle, fearing Jon would recover and reveal the truth about Cersei's children's parentage to King Robert, sends Colemon away and does not properly treat Jon. Jon's death prompts Stannis Baratheon, who had initiated the investigation about Robert's bastards and enlisted Arryn to help him (while in the TV show it was Arryn alone who conducted the investigation), to flee to Dragonstone believing he may by the next target.
Arryn was being treated by maester Colemon, who was going to give him purges to get the poison out, but because Pycelle knew that Arryn knew the secret of Cersei's incest, he sent the man away and just gave Lord Arryn painkillers to ease his passing. Pycelle didn't know who actually poisoned Arryn.
In "A Storm of Swords", Lysa blurts out the whole truth about Arryn's death when she drags Sansa to the Moon Door. Littlefinger tries in vain to hush Lysa, feeling uncomfortable that the secret is revealed in the presence of Sansa and Marillion.
It is not revealed in the novels why Littlefinger wanted Jon dead but he could have several reasons:
- To make Lysa free for marriage and to gain control over the Vale by marrying her;
- To prevent Jon from telling Robert Baratheon the truth about Cersei Lannister's children;
- To turn the Starks and Lannisters against each other by the letter that Lysa sent to Catelyn, in which she falsely put the blame on the Lannisters.