Ser Emmon attended the Hand's Tourney in King's Landing with five of his brothers. When the War of the Five Kings begins, the Freys are persuaded to join Robb Stark. However Emmon takes the Lannisters' side due to his marriage.
During the war Cleos Frey, while accompanying his cousin Jaime Lannister and Brienne of Tarth, is killed in a fight with outlaws on the road between Maidenpool and Duskendale. Shortly after their son Tion is murdered by Lord Rickard Karstark at Riverrun, along with one of Ser Kevan Lannister's sons, Willem.
The Freys with the aid of Roose Bolton, treacherously betray Robb at the Red Wedding, between Robb's uncle Edmure Tully, Lord of Riverrun and Lord Paramount of the Trident, and one of Emmon's half-sisters Roslin Frey. Robb, his mother Catelyn Stark (formerly Tully) and most of their troops are murdered. Many nobles, including Edmure, are captured. For their rebellion against the Iron Throne, the Tullys are stripped of Riverrun and all its lands and incomes, which are granted to Emmon Frey for his support of the Lannisters, creating House Frey of Riverrun.
Walder Frey's grandson and heir, Ser Ryman Frey, leads a Frey force of 2000 that besieges Riverrun, which is being held by Edmure's uncle Ser Brynden Tully, the Blackfish. They are assisted by the new Warden of the West, Ser Daven Lannister, and many of the River Lords are forced to participate in the siege, though unwillingly.
Jaime Lannister is sent to establish Lannister power in the Riverrun. He finds the siege is being poorly handled, with Ryman threatening to hang Edmure each day, but never going through with it as he doesn't want to lose a hostage. Emmon thinks he's been made Lord Paramount of the Trident, but Jaime tells him this title has gone to Petyr Baelish, the new Lord of Harrenhal. Emmon is worried about Riverrun being attacked, as he doesn't want his new castle damaged. He continually reminds people of his new title, showing his letter from King Tommen Baratheon. His wife finally tells him everybody knows about the King's decree.
Jaime persuades Edmure to tell his uncle to surrender Riverrun, threatening to destroy Riverrun and the Tullys if Edmure refuses, and offering to treat him well at Casterly Rock, sending his pregnant wife Roslin with him. However Edmure delays and by the time Riverrun is surrendered, Brynden has escaped by swimming under a gate and down the river. Emmon is furious, threatening to have Edmure beheaded for this. Jaime sends Edmure back to Casterly Rock. Emmon is left to hold Riverrun with a 200 men garrison, though is worried Brynden may try to retake Riverrun. He calls together all the people of Riverrun and gives a long speech about how he will be their new Lord. Unknown to him the minstrel in the camp who is now staying at Riverrun, Tom Sevenstrings, is a member of the Brotherhood without Banners. They are currently being led by Lady Stoneheart, whose intention is to kill anybody connected to the Red Wedding, such as the Freys.
- In the HBO Series Emmon does not appear. Walder Frey is made Lord of Riverrun for the Red Wedding.