Aenys is part of the Frey force that with Roose Bolton takes Harrenhal. After the Battle of the Blackwater, the Freys meet with Roose Bolton, thinking Robb Stark will lose the war. Aenys claims they need to fall back, as they will be unable to hold Harrenhal against Tywin Lannister. Later news arrives that Robb has broken the marriage pact he made with the Freys.
When Jaime Lannister and Brienne of Tarth arrive at Harrenhal, Brienne says she needs to return Jaime or Catelyn Stark's daughters will die, which Aenys is dismissive of. The Freys agree to rejoin Robb's cause if his uncle Edmure, Lord of Riverrun, marries Roslin Frey, a half-sister of Aenys. However they have secretly made an agreement with Tywin. The wedding takes place, but at the reception Robb, his mother Catelyn, and most of their army are murdered by the Freys and Boltons.
Roose Bolton is made the new Warden of the North and his bastard Ramsay Bolton is legitimized and betrothed to "Arya Stark" (really Jeyne Poole) to legitimize the Bolton claim to Winterfell. With his own forces Roose takes 400 Frey cavalry and at least a thousand Frey men under Ser Aenys Frey and one of their half-brothers Ser Hosteen Frey north, to assist him against Stannis Baratheon and the Ironborn.
Meanwhile Aenys' younger son Rhaegar and two of Aenys' half-brothers Jared Frey and Symond Frey have sailed to White Harbor to return the bones of Ser Wendel Manderly, who was murdered at the Red Wedding, to his father, Lord Wyman Manderly of White Harbor. A marriage pact has been made, for Wyman's grandaughters Wynafryd Manderly and Wylla Manderly to marry Rhaegar and another of Walder Frey's grandsons Little Walder Frey. Secretly Wyman is plotting to restore rule of the North to the Starks, but had to put on a pretence of compliance with the Freys as his only surviving son Wylis was a hostage of the Lannisters. When Wylis is returned Wyman sends Davos Seaworth , who has arrived in White Harbor to try gathering support for Stannis, to recover Rickon Stark from the island of Skagos. Wyman also tells Davos he will give the trio of Freys with him palfreys as guest gifts, which under the rules of guest right means they are no longer under the protection.
The wedding between Ramsay and "Arya" is intended to be held at Barrowton. Wyman arrives but Rhaegar, Jared and Symond Frey have vanished, Manderly claiming they rode on ahead due to the slowness of his train. Ramsay searches but is unable to find them. Roose hears that Stannis Baratheon has taken Deepwood Motte from the Ironborn and is gathering support. He thus decides to hold the wedding at Winterfell, forcing Stannis to battle and establishing the Bolton claim to Winterfell.
At the wedding Wyman Manderly serves three huge meat pies to the Boltons and Freys. Wyman asks for a song of the Rat Cook, who served to a King who had wronged him a pie containing his son. He was punished by being turned into a rat that could only eat its children for murdering a guest. These imply that the missing Freys were present at the wedding after all. Big Walder Frey thinks that Wyman had the Freys travelling with him murdered, and later Hosteen Frey accuses Wyman of their murders, which Wyman laughs at.
A series of murders happen at Winterfell, including Aenys Freys' squire, who is found naked and dead of exposure in the old castle lichyard. Though Aenys claims he got drunk and lost in a storm, Theon Greyjoy wonders why he would take off his clothes to go outside. Aenys accuses Theon of the murders, till Barbey Dustin states he lacks the will. Aenys then suspects Lord Wyman Manderly off the crimes. Barbrey Dustin says that many of the Northern Houses lost kin and men at the Red Wedding, and tells him "The north remembers, Frey." Aenys Frey claims Robb dishonoured tbe Freys and the northmen had best remember this.
Later a fight breaks out between the White Harbor and Frey men, when Hosteen accuses Wyman of the murders, including that of his nephew Little Walder Frey. Wyman insults the Freys, at which Hosteen attacks Wyman, almost killing him. To prevent further trouble, Roose sends the Freys and Manderlys out to fight Stannis, having received his location from a map sent by Arnolf Karstark.
Aenys and Hosteen lead a force out of the main gate of Winterfell. While this is happening Theon rescues Jeyne Poole by jumping with her off the walls of Winterfell. They are found by Mors Umber, who has joined Stannis. Mors' boys have dug pits which have been covered by the heavy snows. When the Freys leave the main gate they ride into the traps, and Aenys breaks his neck. Command of the Frey force falls to Hosteen, who only lost his horse and is angry now. When Stannis hears this news from Theon he smiles, and implies he has a plan to defeat the Freys. It is theorized Stannis intends to trick the Freys into changing onto a frozen lake.