An oceanic planet is discovered. Scientists on Earth create a cyborg mermaid and have a little girl remotely pilot it, in order to explore the planet. It turns out that a good deal of the life in the ocean is hostile.
Vacant Ark contains examples of the following:
- Bullet Catch: A critical part of the gameplay.
- Bullet Hell
- Downer Ending: The girl controlling the blue mermaid ends up catatonic with vacant eyes.
- Duel Boss: The red-haired mermaid also has a force device, and uses red crystals for ammunition.
- Easy-Mode Mockery: The Shallow game ends after the first stage.
- Evil Counterpart: The red-haired mermaid
- Fetus Terrible: Embryos/fetuses are recurring enemies.
- Idiosyncratic Difficulty Levels: Shallow, Middle, Deep and Abyss.
- Nintendo Hard
- Recurring Boss: The red-haired mermaid, although she usually has another boss in front of her until the final stage.
- Shout-Out: One of the music tracks is named "Zunchacha" for a major Taito music composer, Zuntata
- Timed Mission: Some of the bosses will leave if you take too long to defeat them.
"Return to Earth. You are not invited to here..."