It stars the Kobinata siblings: A young boy named Yuu, and his older sister Aya. These siblings love and care for each other so much that it somehow causes a rip in the time/space continuum during a beach trip, sending them both into a different dimension. Turns out this was the work of the evil Aquris, who rules over this new world and tried to pull one sibling from the other into this world, but ended up taking them both instead. So he curses Aya to be constantly captured and trapped inside giant cube-shaped water tanks that are found in this bizarre new dimension.
It's up to her little brother, Yuu, to save her from her watery prisons before she drowns, all while making sure he doesn't drown, himself. This will involves a lot of block-pushing, utilizing switches to raise and lower the water level, and avoiding contact with any and all dangerous obstacles he comes by. Later on, the brother and sister end up switching roles, turning Yuu into the hostage and Aya into the one that must rescue him.
Being one of Fox Eye's first games (and one Fox would love to eventually make a sequel to), this game set the standard for underwater-based gameplay and Oxygen Meter maintenance that Fox and his development staff would be known for in his games as the most prominent part of their challenge (among other things). This has shown well in his later games such as Holdover, Sacrifice Girl, and Hades Vanquish. The game's two-character management style eventually returned in Fox Eye's event-only title, Natica and Sandy: Underwater Rescue.
Aqua Cube contains examples of:
- 2½D: It's in the title that all of the game's stages take place on giant cubes of water, but despite the graphics being 3D, movement is restricted to 2D as your character can only travel around each cube's perimeter. This means that pushing blocks into a corner of the cubed-shaped level will cause them to get stuck.
- Author Appeal: This is one of Fox Eye's very first games, and as such, one of the first games to show you the developer's love for underwater exploring and the risk of drowning, which has been seen in all of their future games since.
- Big Eater: Yuu's bio says that "He eats a lot".
- Big Bad: Aquris, a nasty, love-hating, fairy-like being that rules over the other dimension and is responsible for Aya's (and later Yuu's) curse of constant imprisonment.
- Cool Shades: One of the enemies are fish that sports these. In a prototype comic, one accidentally bumps into Yuu underwater and knocks him unconscious because he was lonely and looking for someone to talk to, not realizing that the boy was drowning. After Aya rescues Yuu, the sunglasses-wearing fish ends up in a similar situation where an angry Aya knocks him onto dry land and makes him flop around to breathe water.
- Early Installment Weirdness: Being one of Fox Eye's two 2008 releases (the other being Blue Port), and Fox himself having created several games under his own circle for over 10 years, Aqua Cube has remained the only Fox Eye game that features a playable male protagonist (Yuu), as all of Fox's other games only feature female protagonists. Even then, Yuu eventually switches roles with his older sister, Aya, and Aya becomes the playable lead, instead. This was also the only Fox Eye game for a long time that made you manage two Oxygen Meters at once until this came back in Natica and Sandy: Underwater Rescue, almost 10 years later.
- Fanservice: The very limited and rather-skimpy swimsuits both siblings wear are stated to count as this toward their opposing gender of players: Aya for boys and Yuu for girls. Amusingly, the page image is a cropped image of the siblings wearing translucent t-shirts over their swimsuits as a teaser. The shirts otherwise don't exist anywhere else in and outside of the game.
- Fragile Speedster: Aya compared to Yuu once she's playable. She can jump higher and run faster than Yuu, allowing her to leap greater distances over dangerous obstacles. She still dies from one hit just like her brother, though.
- Hoist by His Own Petard: There's no way you can attack Aquris directly when you first face him. You must dodge his blasts while finding a switch to raise the water, then dive into it. The water will reflect his blasts right back at him for a One-Hit KO.
- Instant-Win Condition: If the trapped sibling is on land when they're freed, the level is won. However, if they're released underwater, they must then follow you back to the surface so both of you can breathe before the level can be beaten. This means that even if you've freed Aya with Yuu in this case, either one of them can still drown and net the player a Game Over within the amount of time it takes Aya to swim with Yuu back to the surface for air.
- Level-Up at Intimacy 5: Actually precedes BLUE GUARDIAN: Margaret of this trope in a Fox Eye game. As Yuu performs certain actions (such as pushing blocks or giving Aya a Breath of Life Underwater Kiss), it raises his excitement. However, the higher it is, the faster his Oxygen Meter will drop while he's underwater.
- The One Guy: As stated in Early Installment Weirdness, Yuu is currently Fox Eye's only male protagonist. Future Fox Eye games have utilized male characters only as NPCs and Mission Control, while Yuu remains the only male in a Fox Eye game to actually be playable.
- One-Hit-Point Wonder: If anything harmful touches the siblings just once, Game Over.
- Oxygen Meter: The well-established staple of Fox Eye's games. This game has you manage two of them: The shrinking bubble representing the controlled sibling's air, and an animated portrait that appears for the captured sibling whenever he or she is submerged. Their portrait will struggle around harder the closer they are to drowning, essentially making their meter a Timed Mission if the water can't be dropped again before they drown.
- Promoted to Playable: Later levels of the game turn Aya into the playable protagonist when Aquris switches to capturing and tormenting Yuu, instead.
- Purple Is Powerful: Aquris mostly wears purple, and is constantly using his power to kill the siblings slowly, if not outright directly if the battles with him are anything to go by.
- Trademark Favorite Food: Yuu loves curry rice, while Aya loves melon parfaits.
- Underwater Kiss: You must perform this technique on the captured and submerged sibling to replenish their Oxygen Meter and keep them from drowning, but this is taken out from the oxygen of the sibling you're currently using, meaning doing this for too long ends up drowning that sibling, instead. Later stages will prevent this tactic by locking the captured sibling inside a cage rather than just restraining their arms and legs.
- Video Game Caring Potential: The game makes it a head to have you figure out how to save the captured sibling without bringing them any harm. For example, certain block-related puzzles, if done incorrectly, could lead to Yuu accidentally dropping a heavy block right on Aya, leading to an instant Game Over.