The movie starts off in a night battle with Aoba, Kinugasa, Choukai Kai 2, Furutaka Kai 2, Kako Kai 2, and Tenryuu fighting off the abyssal fleet. After the battle, the fleet receives a kanmusu "drop" which happens to be the Kisaragi that sunk in the Kancolle Anime. After the battle, the kanmusus welcome back Kisaragi and have a party. Despite having Kisaragi back, some the kanmusu including Nagato and Kaga were not too happy having Kisaragi back. This is because Kanmusus that have sunk will have a to be revived back as an abyssal ship, and Kisaragi started to physically have attributes of an abyssal ship.
-lots of dialogue here about what to do with Kisaragi-
The movie goes on, and the Kanmusus stumble upon a part of the sea where their equipment start to deteriorate once entered. Turns out, there's a abyssal ship base located around that area, and the Kanmusus decide to counteract it somehow. Nagato figures out that Fubuki, is needed to complete the mission (due to Fubuki being the only one not having a negative impact on her equipment). Nagato then sorties out the kanmusus in order to defeat the abyssal base.
-lots of battling happens-
Fubuki reaches the final point, and finally stumbles on the abyssal base where she meets "Abyssal Fubuki." Abyssal Fubuki then tells normal Fubuki that this fight is meaningless. Where Kanmusus are just fighting with themselves, and it's an endless loop. The Kanmusu that sunk become abyssal ships, and abyssal ships that are defeated can become regular Kanmusu again. Although, Fubuki doesn't give in, and tells Abyssal Fubuki that no one will sink again, so everyone can become a Kanmusu. After that, Fubuki purifies Abyssal Fubuki and that part of the sea returns to normal.
The movie ends with all the Kanmusus returning back to the base without anyone sinking.