Flynn is a four thousand-pound English elephant seal with a heart of gold and a head of sand. He is as passionate about being a pirate as he is clueless. He doesn't know his port from his aft, and almost never remembers that being a sea creature means he can swim. However, he makes up for what he lacks in intelligence with an abundance of enthusiasm.
Flynn was found in the English Channel and later recruited by Captain Gutt. He loves being a pirate and takes his job with joy.
One day, while out at sea, Flynn, along with the others in the crew, watched as their captain pulled a saber-tooth squirrel out of the ocean waters after harpooning the acorn shell that the squirrel was holding: the squirrel, named Scrat, was found half-swallowed by a small fish and used for entertainment aboard the ship.
Not long after, Flynn and the others encountered a group of animals lost at sea aboard a drifting ice floe: a mammoth named Manny, two sloths named Sid and his Granny and a Saber-Tooth Tiger named Diego. Remarking that they looked "fluffy", Flynn stood by for his captain's orders as Gutt appeared, introducing himself to the castaways, claiming that they were lucky to be found by Gutt and his crew before pirates found them first. Manny called out that they only wished to reach the continent and his family, to which Gutt coldly replied that there was no way back. At that, Flynn chimed in, calling out that there was a means of returning to the continent: Switch-back Cove provided an ocean current that could take them back to the mainland, all much to Gutt's chagrin, who quickly silenced the seal with a sharp stomp on his tail fin.
Gutt then ordered his crew to attack the castaways, with Flynn helping by allowing Gupta, a badger and fellow pirate, to bounce off his belly and up a mast so as to "fly the colors". During the fight, Flynn leapt down from the ship, flattening Sid with a belly flop.
When the captives escaped and brought down the iceberg, Flynn panicked, thinking he was going to drown, until Gutt reminded him he was a sea creature. When Flynn asked about the missing Shira, Gutt disregarded her, telling Flynn to push the piece of ice the crew were resting on out to sea.
In the final battle, Flynn easily withstood Sid and Granny's attempt to hurt him. He and Gupta chased them to the edge of Gutt's new iceberg, but were scared off by Granny's pet whale, Precious. Soon after, Precious blasted Flynn, Raz, and Dobson into the water with her spout. Flynn found the experience quite enjoyable, and thanked Precious for it before falling into the cold waters below. It's unknown what became of Flynn after Gutt's apparent death, but chances are that he survived, as he was knocked into the sea but is still a sea creature. However, given that the crew has been most likely disbanded afterwards, it's presumed that Flynn parted on different ways.