"Pokémon 3D Adventure 2: Pikachu no Kaitei Daibōken" is a short anime film that serves as a sequel to the earlier 3D Pokémon adventure. The story centers on Pikachu and its friends as they embark on an underwater journey to rescue a group of Pokémon trapped in a sunken ship. The adventure begins when a mysterious submarine emerges near the shore, capturing the attention of Pikachu, Togepi, and other Pokémon. Curious and concerned, they investigate and discover that the submarine is operated by a robotic Pikachu, which leads them to the underwater wreckage.

As the group ventures deeper into the ocean, they encounter various aquatic Pokémon, including a friendly Wailmer and a school of Remoraid. The underwater environment is vividly depicted, with the sunken ship serving as the central setting for the rescue mission. Inside the ship, the Pokémon face challenges such as navigating through dark corridors, avoiding traps, and solving puzzles to free the trapped Pokémon. The robotic Pikachu plays a key role in guiding them, though its origins and purpose remain enigmatic.

The narrative emphasizes teamwork and bravery as Pikachu and its friends work together to overcome obstacles. The trapped Pokémon, including a distressed Corsola, are eventually freed, and the group returns to the surface. The film concludes with the robotic Pikachu departing, leaving its true nature and intentions unresolved. The story is straightforward, focusing on adventure and camaraderie, with minimal dialogue and a strong reliance on visual storytelling to convey the emotions and actions of the Pokémon characters. The underwater setting and the use of 3D animation provide a unique visual experience, distinguishing it from other Pokémon media.