The submarine is owned by the Shell Lodge Squad via the Penguins. It was first used in the series to hunt down the Snakehead Trout. It was also used in the series on several occasions when the Penguins need to travel in the ocean.
The Lodge once used the sub to survive when Alice starts crying in her massive size. Her tears flooded the room, and the Lodgers had to use the submarine to avoid being washed away.
The sub is big enough to fit the entire Lodge, and has missile launchers. The Lodge uses it whenever they need to travel in oceans, despite some Lodgers capable of breathing underwater.
Kowalski and Sandy discussed once that they might need a way to keep the sub and bring it up at anytime. So, they both put a special device that can shrink it, and trap it in an indestructible metal ball. Now, with this, the Lodge can activate the sub at anytime by pressing a tiny button on the ball, and bring up the sub.