At the end of the previous episode, the St. Anne overturned and sank into the sea, taking Ash, his friends, and Team Rocket down as well. The next morning, a police ship pulls up at the location. Officer Jenny gives a short speech to commemorate the missing characters, presumed dead. She tosses a bouquet of white flowers into the sea of debris as a memorial. Jenny and the other officers salute, and one plays the trumpet as the flowers sink underwater. Meanwhile, Misty, Brock, and Pikachu call to Ash to wake him up. Misty points to the porthole and Ash looks out, noticing fish swimming. He realizes that the ship has sunk, the image panning out and showing the ship upside down atop a seamount, positioned at the mouth of a trench.
Meanwhile, Jessie and James wake up from being knocked out as well., They run out into the hall and notice everything upside down. Meowth informs them that the ship capsized and sank. James panics as Jessie brings out Ekans. She orders it to use Acid to open a hole in the floor. Meowth tries to stop her, but is too late. The attack opens a hole, through which water begins to shoot as the ship rumbles. Jessie and James try to block the jet of water, but fail, as the water fills the hall and washes Team Rocket away. Elsewhere on the ship, Ash and his friends head out into the stairwell, the water level preventing them from going to the deck. Misty notes that the ship will take time to fill with water, but time is still critical. Ash wants to dive down to the deck, but Brock says that it could be dangerous. Ash realizes he is right, as he has a vision of running into a locked hatch and drowning. Misty sends out her Goldeen to scout the hall. It swims down and finds a dead end, but runs into the members of Team Rocket, who are again unconscious.
As Ash and his friends wait for Goldeen, James’s head pops out of the surface, scaring them. Goldeen then comes into view as it pushes Team Rocket, who are blue in the face from nearly drowning, up onto the deck. Jessie and James regain consciousness and stand up, ready to battle. They send out Ekans and Koffing as Ash and Brock send out Charmander, Squirtle, Bulbasaur, and Geodude. Before any of them can launch an attack, the ship begins to tip, sending everyone sliding. Ash orders the Pokémon to go to the other side, but it causes the ship to tilt the other way. After sliding back and forth, Misty orders everyone to recall their Pokémon and forget the battle in order to survive. They do so and the ship regains balance. Misty finally manages to convince everyone to work together temporarily. With the truce, Misty reveals that she knows the ship blueprints, because she once built a model of it, and that they should go up to the bottom of the ship and cut through the hull to escape. They approach a staircase, and Brock sends out Onix to allow everyone to climb up.
The ship's lights begin to fail as the group approaches a darkened portion of the hall. Ash brings out Charmander to light the way. They enter the next room and find it impossible to cross over to the engine room hatch due to the large gap and the raging fire below them. Ash has Pikachu shock him to get him to think. He then sends out Bulbasaur to use Vine Whip to create a bridge to the opposite hatch. Ash and his friends begin to slowly cross the vines, but James is too scared to cross, begging Jessie and Meowth to go on and leave him behind. Jessie slaps him and helps him regain his composure, but Ash and his friends are already across. Jessie orders Bulbasaur to send back the vines. Eventually, everyone makes it safely to the engine room, though Team Rocket is virtually exhausted. Ash brings out Charmander to use Flamethrower to cut an opening through the hull. Misty instructs everyone to strap onto a Water-type Pokémon, but Team Rocket doesn't have one. The hull opens and water pours in. Ash recalls Charmander, who is running from the water. Ash and Pikachu strap onto Squirtle while Misty gets Goldeen and Brock gets Starmie. While Ash and his friends swim into the waterfall and escape to the surface, Team Rocket is still stranded. James suddenly starts snickering, as he reveals the golden Poké Ball holding his Magikarp, which has proved useful after all. Team Rocket straps onto Magikarp and attempt to escape, but they find that Magikarp can't swim. The water picks up and washes the ship into the trench, leaving Team Rocket's fate unknown.
Ash and friends climb onto a makeshift platform, noticing Team Rocket hasn't yet made it to the surface. Ash looks out to sea and is unable to spot any land. Brock brings up the story of Noah, sending out a bird to search for land and Ash does the same thing by sending Pidgeotto out to scout. Pidgeotto flies out and finds Team Rocket on the surface, still attached to the splashing Magikarp. Pidgeotto brings them back to the platform, and Ash and his friends presume that they have passed on. They attempt to push them back into the sea as a traditional burial, but Jessie and James wake up just in time to prevent their accidental drowning.
The two groups have no choice but to stay on the platform for the night. They wake up the next day and all are starving. Everyone immediately thinks of the Magikarp as their first source of food, Meowth attempts to bite it but ends up breaking his fangs, as Magikarp is, according to Misty, only scales and bones. At this point, James is so frustrated with his Pokémon that he kicks it into the ocean. The Magikarp begins to glow as it evolves into a Gyarados. Ash checks his Pokédex as James attempts to reclaim his role as the Pokémon's master, but is too scared of it. Misty sends out Goldeen, Staryu and Starmie. Brock thinks she will battle it, but she only plans to run away, with the Water Pokémon pulling the platform as everyone else attempts to row. Gyarados begins to pursue them, but suddenly stops. They think it is tired, but Misty remembers Sailor stories about Gyarados’s Dragon Rage attack. The waves pick up as more Gyarados appear. They swim in a circle, forming a powerful water cyclone. The Gyarados advance towards the raft. Brock urges everyone to flee again, but Misty says that nobody has ever survived the attack before. The attack sends everyone spiraling into the cyclone. Ash and his friends try to hold together, but they lose grip and spiral out of control.