At some point before Race to the Edge, Viggo Grimborn and his Dragon Hunters captured Shipsbane, and kept the dragon to use at a later date.
In "Dire Straits", Viggo, tired of constantly being defeated by Hiccup and his Dragon Riders, decided to use Shipsbane to his advantage. He chained the dragon to the seafloor of the Straits of Baldur with dragon-proof chains in an attempt to cut off all of Berk's trade and starve the people, forcing Hiccup to chose between the safety of the village and defeating Viggo. Shipsbane used his whirlpool to attack a group of traders coming to Berk, killing all of them except for Trader Johann, who was able to avoid the whirlpool due to prior experience with Submarippers. Johann told Hiccup and Stoick about the event, enraging Hiccup. He and the Dragon Riders headed to the Straits of Baldur, where they found the Submaripper attempting to suck an adolescent male Scauldron into his whirlpool. The riders saved the Scauldron and dove underwater on their dragons to see the cause of the problem. When they encountered Shipsbane, they noticed that he was chained to the seafloor and tried to free him, but the dragon kept attacking them. Unable to stay down underwater long enough to break the chains, Hiccup created the Diving Bell and used it to reach the seafloor. He used Changewing acid to break the chains, as it could burn through dragon-proof metals. Unfortunately, the Dragon Hunters soon arrived, and they woke Shipsbane up by launching rocks from their catapults to create vibrations in the water to rouse up the Submaripper. Shipsbane tried to attack Hiccup, as he believed he was trying to hurt him. Fortunately, however, Hiccup was able to free the dragon from the chains, but the Diving Bell was broken with Hiccup trapped inside it. With Toothless unable to save him, Shipsbane, in gratitude for Hiccup saving him from the chains, picked up the Diving Bell in his jaws and carried it to the surface, where he deposited it on the Rider's boat. Shipsbane then surfaced and roared his thanks before he dove back into the open ocean.
Shipsbane returned in "Shell Shocked, Part 2", where he was summoned when Viggo, who was "working" with Hiccup and the Riders in an attempt to stop Ryker Grimborn and the Shellfire, dropped a dagger into the water, creating vibrations that attracted the dragon. He then fought the Shellfire, the battle ending with Shipsbane knocking the metal Dragon Hunter ship off of his opponent's back. As the Shellfire swam away, Shipsbane created a whirlpool and sucked the metal ship and Ryker in, killing the Dragon Hunter. Shipsbane then swam away deep into the ocean, never to be seen again.
Shipsbane looks very similar to a normal Submaripper. He is very large in size and has several sharp teeth in his mouth. He is light green in color with several dark green splotches and stripes all over his body, legs, and tail. He has several, orange-tipped plant-like growths on his back and tail.