He died in mysterious circumstances just prior to the events of the series. He is played by guest star John Standing and appears only as a corpse in the series premiere. He was the Lord of the Eyrie, Warden of the East, Defender of the Vale, and Hand of the King to Robert Baratheon.
Jon Arryn was the Lord of the Eyrie and the head of House Arryn, one of the Great Houses of Westeros. Jon was the Warden of the East and Defender of the Vale. He was a respected nobleman and both Eddard Stark and Robert Baratheon were fostered by him during their adolescence. The Mad King condoned the kidnap of Eddard's sister and Robert's betrothed Lyanna Stark. The Mad King had Eddard's father and brother killed for protesting against the kidnapping. When he then demanded that Eddard be turned over to the King's justice, Lord Arryn rebelled, calling his banners to war. House Stark and House Baratheon followed suit. The rebels forged an alliance with House Tully through marriage, with Eddard married to Catelyn Tully and the then-elderly Jon to the young Lysa Tully.
After the rebel victory in the war, Robert became King and appointed Jon as his Hand. Jon served the realm well for many years as Hand of the King. Indeed, Jon Arryn was essentially the man really holding the realm together for the next seventeen years, while Robert drank and ate and used whores.
Jon Arryn died in King's Landing immediately prior to the events of the series, sparking King Robert's search for a replacement. Jon is survived by his wife Lysa and their six-year-old son, Robin Arryn. Jon was investigating the legitimacy of the children of Queen Cersei Lannister, and just before he died discovered that they were secretly not the biological children of Robert Baratheon.
His dying words were to Robert Baratheon, "The seed is strong."
Jon Arryn's body is laid out in state in the throne room of the Red Keep in King's Landing. Ser Jaime Lannister and Queen Cersei discuss Jon's attempts to learn the truth about their incestuous relationship and his failure to do so. Later, news of Jon's death reaches Eddard Stark at Winterfell, who is shocked and upset as he considered Jon to be a second father to him. Catelyn then receives a letter from Lysa accusing House Lannister for murdering Jon.
When Eddard Stark attends his first Small Council meeting in King's Landing, he is shocked to learn that the realm is six million Gold Dragons in debt, and refuses to believe that Jon Arryn would let this happen. Grand Maester Pycelle and Renly Baratheon explain to Lord Stark that while Jon gave wise and prudent advice, King Robert did not always follow it.
Arryn had asked Pycelle for The Lineages and Histories of the Great Houses of the Seven Kingdoms, a book detailing genealogies of the nobility, which notes the heredity preponderance for black hair in House Baratheon.
Eddard Stark is told that Arryn visited with an armorer, Tobho Mott, several times before his death and also talked with his apprentice Gendry, inquiring about his mother. Stark immediately realizes upon meeting with Gendry that he is King Robert's bastard son. On the day he died, Arryn met with Mhaegen, a prostitute at Lord Petyr Baelish's brothel. She showed him her infant daughter, Barra, who was fathered by King Robert Baratheon.
Varys privately warns Eddard that he thinks Jon Arryn was murdered by an unknown party for asking too many questions, using a rare and untraceable poison known as the Tears of Lys.
Under forceful interrogation by Tyrion Lannister, Grand Maester Pycelle confesses that he knew that Jon Arryn had unearthed the truth upon seeing Robert's bastard children that Queen Cersei's three children were not conceived by Robert, but by her twin brother Jaime Lannister. Pycelle states that Jon Arryn intended to act and reveal his discovery to King Robert. When Tyrion accuses Pycelle of having Jon poisoned to keep the truth from getting out, he angrily denies that he killed him. Tyrion then points out that Pycelle must have realized that someone had poisoned Arryn (and he wasn't simply sick), but he let him succumb anyway, so he has Pycelle thrown into the Black Cells.
After being reunited with Petyr Baelish, Lysa obsessively declares her love for him and the things she has done to demonstrate it, including lacing Jon's wine with Tears of Lys and then sending a letter to Catelyn accusing House Lannister of the assassination.
Eventually, Petyr is forced to answer for his many crimes, including his role in the Assassination of Jon Arryn, when Sansa Stark unexpectedly puts him on trial. Sansa publicly accuses Petyr of persuading Lysa (whom Petyr also murdered) to poison Jon with Tears of Lys and write a letter to her sister Catelyn, falsely accusing the Lannisters of killing her husband, igniting the conflict between both great houses. When Petyr's guilt becomes plain for all to see, his cries for mercy are coldly rebuffed by Sansa, who has her sister Arya Stark slit his throat, exacting justice for Jon.
Foster father of both Robert Baratheon and Ned Stark, jon Arryn served as Robert's Hand of the King until his untimely death. He was married to Lysa Tully, the younger sister of Catelyn Stark, a marriage that bound his family with Ned's during a time of war.