Part of the initial appeal of Game of Thrones is that, briefly, during season 1, the show acts as a murder mystery.
In both the series and its initial source material, George R.R. Martin's A Song of Ice and Fire novels, Ned Stark (Sean Bean) is, at first, reluctant to accept King Robert Baratheon's (Mark Addy) offer to become Hand, replacing his recently deceased mentor, Jon Arryn (John Standing). However, after Ned's wife Catelyn (Michelle Fairley) receives a letter from her sister Lysa (Kate Dickie), who says that she suspects her husband was murdered, Ned changes his mind, becoming Robert's new Hand and venturing to King's Landing to investigate.
As such, a majority of Ned's early scenes in the series feature him looking into Jon's death. However, Ned famously gets himself killed early on into the series. With his death, and the subsequent War of the Five Kings, the mystery of Jon Arryn's murder falls to the wayside.
Game of Thrones finally answers the question of Jon Arryn's death in season 4, three seasons after it felt important. While this may seem frustrating for overeager fans who just want to learn what happened, extending this mystery actually helps illustrate one of the show's key themes.

Who killed Jon Arryn?
Game of Thrones finally answers the question of who killed Jon Arryn in season 4 Episode 5, "First of his Name." After helping Sansa Stark (Sophie Turner) flee the scene of King Joffrey Baratheon's (Jack Gleason) murder, Littlefinger, a.k.a. Petyr Baelish (Aidan Gillan) takes her to the Vale, the ancestral seat of House Arryn, under the guise of his niece Alayne. There, Sansa meets her Aunt Lysa and cousin Robin (Lino Facioli).
In a private moment, Lysa asks Petyr if they can finally marry. When Petyr is reluctant, Lysa recounts several of her acts of love for him, including poisoning her husband and framing the Lannisters in her letter to Catelyn. As such, audiences finally learn that Littlefinger was responsible for Jon Arryn's murder this entire time.

Why did Game of Thrones take its time with this reveal?
By the time Lysa drops this bombshell on the viewers, Ned Stark has been dead for nearly three seasons, and viewers likely hadn't thought about Jon Arryn in ages. It might seem like it's too late to answer this question.
However, that's precisely the point that Game of Thrones makes by waiting so long. By now, Littlefinger has officially escaped any consequences for Jon Arryn's murder. He's officially gotten away with it. As he famously says, "Chaos is a ladder," and Jon Arryn's death led to plenty of chaos, allowing Littlefinger to climb higher and higher.
At the time of Jon's death, Petyr was the Master of Coin for Robert Baratheon's small council. By now, he has risen through the ranks to become Lord of Harrenhal and Lord Protector of the Vale, utilizing the crisis of succession, wars, and murders to fuel his ascent.
Meanwhile, Ned Stark, the primary detective into Jon Arryn's death, is now long dead, in no small part thanks to Littlefinger's treachery. If Ned, as a character, represents honor, then Littlefinger represents chaos. As such, Littlefinger's defeat of Ned, a point reiterated long after Ned has left the show with this reveal, showcases how chaos, deception, and cunning outmatch honor in the twisted world of Westeros.

The eventual death of Littlefinger
Despite Littlefinger's initial success, he eventually receives his comeuppance. In season 7, after the Stark children, Sansa, Arya (Maisie Williams), and Bran (Isaac Hempstead-Wright) have reunited in Winterfell, they are able to piece together Littlefinger's true nature, in part due to Bran's greensight abilities.
After a failed attempt to sew discord between Arya and Sansa by turning them against each other, the siblings reveal to Littlefinger that they know of his crimes. Despite his pleas, Arya executes him for his misdeeds, including Jon Arryn's murder, finally putting Game of Thrones' first central plot line to bed.
Although most fans agree that Littlefinger has become too clumsy for his own good at this point, it is worth noting that it takes Bran's magic powers to catch him. Ultimately, he escaped punishment for seven seasons, outplaying just about everyone. Despite not surviving the series, Littlefinger proved he could outwit even the audience, distracting viewers with his chaotic creations to the point where Jon Arryn's death felt like an afterthought until Lysa's revelation.
For more from the world of Westeros, make sure to stream House of the Dragon and A Knight of the Seven Kingdoms on HBO Max.
