At the beginning of the game, the ship is attacked and abducted by Shadow Lugia, throwing two crewmen overboard. According to ONBS, these crewmen had not been found three days after the incident and there are no future reports suggesting they have ever had been. Due to a momentary loss of control over Shadow Lugia, the ship ends up falling in the middle of a desert. This results in Cipher having their AdminSnattle take over the nearby Phenac City in order to keep its citizens from interfering with Admin Gorigan's mission to recover the Pokémon aboard the ship and have them be taken to the Cipher Key Lair in the north in order to turn them into Shadow Pokémon.
When the player first learns of Cipher's activities in the desert, they are unable to reach the location due to their scooter's tires getting stuck in the deep sand. After the scooter is upgraded into a hover scooter, the player is able to reach the shipwreck in the desert. There, it is revealed that Gorigan's recovery operation has been completed, with only a single Pokémon having managed to escape. After the player has defeated Cipher Peon Smarton, they meet a Worker who had randomly stumbled upon the ship and made his home there. On his request, the player then investigates the odd noises he's been hearing from inside of the ship. The cause of the noises turns out to be the sole Pokémon missed by Cipher, a Bonsly, which will run away from the player if they approach it too fast. Just when the player is about to sneak up on Bonsly, they will receive an email on their P★DA, the alarm noise scaring Bonsly and causing it to leave the ship. It can later be found and caught at a random Poké Spot, after which it's returned to its owner at ONBS.
Once the player tries to leave the ship after Bonsly has run away, a group of Team Snagem members ambush them upon their exit and steal their Snag Machine.
Later in the game, a TV report reveals that authorities have also found the ship.
Spoilers end here.
To fully explore most of the ship, the player must push several heavy crates around, not unlike the Strength puzzles in the core series games. The player can use the bed on 4F to fully heal their Pokémon at any time.
Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.