Captain Gills was in the ownership of a young Flip-Flopian named Pook of the Flipside. However, during the events of Chapter 4, Mario and company entered Outer Space and cannot breathe needing a space helmet. They can then talk to Pook who is willing to let them use the Goldfish Bowl but only after they release Captain Gills into the water (as he has gotten too big for his bowl). Mario can then take Captain Gills to the basement floor and release the fish into the water next to the bar. Captain Gills grows as the game progresses becoming even bigger. He may have became a carnivore as bones of other fish are seen by him.
After the game has been completed, Mario can revisit Captain Gills to find that he now has five children of his own. His children are:
- Gills Jr. - Captain Gills' first born son. He is shown to care for his siblings very much and is always seen swimming at a higher altitude.
- Gills II - Captain Gills' second born child and his only daughter. She is often the peacemaker of the group always trying to settle arguments between her brothers.
- Gills III - Captain Gills' third born child and is considered the troublemaker of the group. He is often the cause for his father's lack of sleep.
- Gills IV - Captain Gills' fourth born child. He often tries to lead the back but cannot keep up due to his smaller fins.
- Gills V - Captain Gills' fifth and final born child. He is the youngest of the siblings and often swims behind his brothers and sister.