During the Greyjoy Rebellion, the Iron Fleet led by Lord Euron Greyjoy raids Lannisport, destroying the Lannister fleet. The Iron Fleet was later defeated by the forces of Lord Stannis Baratheon. Following the Siege of Pyke, the Ironborn ruler Balon Greyjoy sues for peace and submits to King Robert Baratheon. His youngest son and heir Theon Greyjoy is sent to live as a ward of Lord Eddard Stark.
During the War of the Five Kings, Balon sends his daughter Yara Greyjoy to attack Deepwood Motte in the North with a fleet of thirty ships. Meanwhile, Theon is made the captain of a single ship called the Sea Bitch and is sent to raid fishing villages. He struggles to win the support of his crew until he finds help in the form of first mate Dagmer "Cleftjaw". Dagmer leads a feint attack on Torrhen's Square. This allows Theon to capture the northern seat of Winterfell with twenty men. Theon is later betrayed by his crew who hand him over to House Bolton.
At the Kingsmoot held after the death of Balon, Yara vows to build the "mightiest fleet" to conquer the mainland. However, she is outmanuevered by her uncle Euron, who advocates forging an alliance with Daenerys Targaryen in order to gain access to her dragons. While Euron is being baptized by Aeron Greyjoy, Yara, Theon, and their supporters flee on the best ships in the Iron Fleet. In response, Euron orders his supporters to build another fleet and to kill his niece and nephew.
Yara and Theon's Iron Fleet sails to Essos with the intention of beating Euron to Dany, who lives in Meereen in Slaver's Bay. On the way, they stop for rest and relaxation at the Free City of Volantis. At Meereen, Yara and Theon forge an alliance with Dany and her advisor Tyrion Lannister. In return for recognizing the independence of the Iron Islands and helping them to overthrow Euron, Yara agrees to ferry Dany's army to Westeros and to cease raiding the mainland. Later, the Iron Fleet is seen sailing as part of a combined Targaryen armada to invade Westeros.
In the books
In the A Song of Ice and Fire novels, the Iron Fleet is the elite naval force of the ironborn. It consists of around a hundred warships dipping 100 oars or more. The Iron Fleet is not the entirety of the ironbon naval forces, which are estimated to number well over 500 longships. However, most of these ships only dip 20 oars and are meant for coastal raiding, not pitched naval battles and ship-to-ship engagements. The Iron Fleet is a permanent military force held to belong to the Iron Islands as a whole, not individual captains or houses.
The Iron Fleet spearheads any major military action. Its job is to destroy or pin larger enemy ships, allowing smaller longships to land on the enemy shores. The Iron Fleet was comprehensively defeated in the Battle of Fair Isle during the Greyjoy Rebellion, when the Royal Fleet under Lord Stannis Baratheon and the Redwyne fleet under Lord Paxter Redwyne trapped it in a pincer movement and destroyed it. This allowed the royalist forces to attack Pyke and end the war.
Since the end of the Greyjoy Rebellion, the Iron Fleet has been rebuilt to its former size. It is commanded by Victarion Greyjoy from his flagship, the Iron Victory. Following Balon's death, a Kingsmoot is held and one of his younger brothers, Euron Greyjoy, is proclaimed King of the Iron Islands. Euron then embarks on a massive campaign to conquer Westeros, beginning with the Shield Islands in the Reach. While a section of the Iron Fleet under Victarion draws the Shield Islanders' fleet away from the islands, a larger Ironborn force under Euron raids and pillages the Shields. After capturing Oakenshield, Euron sends Victarion on a mission to bring back Daenerys Targaryen from Meereen. Like the TV series, he intends to marry her as his Queen.