Lilac, Carol & Milla are detained by Neera Li on the Magister's orders, while Torque and his evidence are placed in quarantine. In an attempt to find Torque, Milla digs a hole out her prison cell and enters the Palace's sewer system.
This stage is a water supply and sewage system, and is mostly brickwork, with some patches of dirt Milla can dig into to find crystal shards and other secrets. There are a number of enemies, which are easily dispatched with a well-placed Phantom Block or Shield Burst. Although the Area is maze-like, it is mainly straight-forward. Near the end is a mini-boss battle with a serpent-like creature with a head that looks like a deep-sea diving helmet, the Iron Worm. The hatch opens regularly to spew damaging green slime. But four Phantom Blocks later, it explodes, and the head rolls onto a switch that opens the path to Area 2.
Similar to Area 1, just with the addition of a little more machinery and some swimming. At the end, there is a blocked doorway, and a Phantom Block is required to open it. Once the pathway is open, jump down it and the Mid-Boss battle with Chomper will begin. After defeating said Mid-Boss, a water current will take Milla to the next section of Area 2. After that, there are a few more enemies to fight, and 2 individual switches that change the position of the sewer pipes. Both switches must be pushed once in order to reach Area 3.
Now it's time to climb, using a series of ladders, springs and moving platforms. There are very few enemies to worry about.
Another simple area, but this time there are a few slime pools that need to be navigated. The last slime pool is by far the largest, and this is where the Big Chomper boss fight takes place.
See also: Main Enemy List
- Chomper (Mid-Boss)
- Chomper Snake (Major Boss)
- Iron Worn (Mini-Boss)
- Card Collector (Aqua Tunnel): Collect all 10 cards in Aqua Tunnel.
- Aqua Tunnel Speedrunner: Clear Aqua Tunnel in 5 Minutes.
- After the boss fight, The level won't end if moving Milla to slime water. The level ends only when she is on the moving boat.
- If Milla dies right when the stage complete sign comes, the player will restart from the last checkpoint instead of advancing to the next stage.
- In the 2nd half of Aqua Tunnel, there is a cluster of pipes in the background. These pipes are identical to the Warp Pipes from the Super Mario Franchise.
- Right before the Iron Worm, there's a ground where Milla can dig. Although it indicates there's treasure, there's nothing really despite the reactions of Milla when she finds treasure.
- In the first underwater area after the Mid-Boss fight, there is a rotating platform. If Milla attempts to swim between the platform when it's closest to the ceiling, she'll be crushed to death, and the player will have to restart at the last checkpoint.
- In a chronological timeline, Aqua Tunnel takes place between Sky Battalion and Jade Creek.