Pilot was recruited to the NSS when he was only 15 by Cuttlefish, unaware of the fate that awaited him. He rescued the Great Zapfish from DJ Octavio and decided to stay with the NSS, not having anywhere else to go. After two years of low activity, Pilot and Cuttlefish went on a mission back in Octo Valley where they were ambushed by an Elite Octoling and all three fell into the Deepsea Metro. Pilot and Cuttlefish were seperated and the Octoling lost their memories and was found by Cuttlefish. Pilot found an employee model CQ-80 and rescued Cuttlefish and the Octoling, now named Eight, from being blended by Tartar. Unfortunately, Pilot was hijacked by Tartar using sanitized ooze and was forced to fight Eight. Thankfully, Eight was able to defeat Pilot and free him from Tartar's mind control and save Inkopolis as well, but it would leave permanent scars on Pilot, both physical and mental.

A few months after the Deepsea Metro, Pilot is investigating the Deepsea Metro entrance near Deca Tower when he hears crying coming from within. Inside the Metro, Pilot finds an Octoling who appears to only be half-sanitized. This is French Fry and Pilot brings her up to the surface after talking with her and realizing she's been trapped in the Metro for a long time. The two of them quickly grow close and eventually start dating. French Fry also becomes an unofficial member of the NSS. During an inspection of the NILS statue to make sure nothing is out of place, Pilot finds a sanitized parasite and becomes infected by it, losing his sense of self and becoming controlled by the parasite. He runs away into the surrounding forest and it takes a week for the NSS to find him again. When they do find him, he is completely covered with sanitized ooze from the parasite and it takes the combined force of the entire NSS to knock him out and remove the parasite from him. However, Pilot quickly realizes that the parasite is still within him but doesn't tell anyone, deciding that since the parasite isn't trying to control him and is somewhat capable of communicating, he shouldn't make the others worry.

After the incident with the parasite, Pilot and French Fry decide to move to Splatsville, not only because people are flocking there in droves and leaving the Square behind, but also to leave behind bad memories. Unfortunately, there is no rest for the weary and the Great Zapfish goes missing for a third time. Pilot, now the Captain of the NSS, begins to investigate. However, while working a Grizzco shift for extra cash, French Fry goes missing and fuzzy ooze takes over the crater where the NSS have set up camp. Pilot is beside himself with worry and throws himself fully into his captain duties. Cuttlefish recruits Neo as a new Agent 3 with his smallfry, Taco, and the three of them get through the Crater. After a fight with Octavio, who has not stolen the Great Zapfish for once, the three of them fall into Alterna, with Cuttlefish getting separated from Pilot and Neo. Callie and Marie are called for backup and the group begin beating the kettles in Alterna and clearing away the fuzzy ooze. A radio transmission comes through during a break period and a voice can be heard talking to Cuttlefish. Right before the transmission ends, a second voice can be heard talking to Cuttlefish. It's French Fry's voice.

Pilot and Neo work together to clear out the rest of the fuzzy ooze from Alterna and hurry to the rocket where Cuttlefish and French Fry are being held. Once at the rocket, Cuttlefish gets dehydrated and French Fry is revealed to have been fuzzified by Mr. Grizz who was behind everything. French Fry doesn't remember Pilot and he flies into a rage, the parasite responding to his intense emotions and letting him make extra limbs out of his ink which he uses to physically fight Mr. Grizz. Unfortunately, Pilot loses the fight and can only watch as the rocket loaded with fuzzy ooze is launched into space. Neo follows Mr. Grizz and the rocket with the help of Deep Cut, who have been trying to interfere but teamed up with the NSS after some convincing. Neo successfully defeats Mr. Grizz with the help of DJ Octavio but goes missing after coming back to Earth. French Fry is returned to her senses but she is much different than how she used to act. Pilot throws himself into doing Salmon Run shifts to try and learn more about Grizzco as a whole, and to try and find a way to 'cure' French Fry of her fuzziness.