The AquariumComp is rather reminiscent of the previously seen ZooComp as it does in this case, feature a fairly aquarium-esque design with fish tanks as well. Mechanically-wise the stage also works quite similarly. Several marine animal styled Mr. Progs are lost and the player must return them to their respective cages in order to progress.
To do so the player must find the program and with hints given by the programs (who all have lost their memory), they must identify what kind of animal the program is about and place them on the correct cage. Failure to do so will result in a forced virus battle and the program being returned to where they were previously found.
There is also an added layer of trickery to consider. While carrying a program, on the lower "wateroad" the player uses to progress, several Cyber Sharks will spawn and move around the map. If they manage to catch to the player, the program will be returned to its location, so the player must avoid them and if possible memorize the map's layout for better chances of success. There are also some platforms "above water" which allows the player to be without fear of the Sharks ever reaching. There are two kinds of Shark, blue and red, with the red ones moving faster than blue.
Also while carrying a program, random encounters will be suspended. If in need of help in identifying the respective animals, the player can use the L button to talk to Lan and have him check the cages for information.
After Captain Blackbeard is fired from the Aquarium due to mistreating the animals with fancy and harsh performances, leading to the penguin Plata running away. He orchestrates a hacking of the Aquarium and setting all the animals free in revenge for being fired (along with his own attempt at controlling the water of Cyber City to be on the good terms of the "organization").
As several dangerous animals are set free which are likely prone to endanger human lives, Lan Hikari and MegaMan.EXE are forced to jack in the AquariumComp to activate the "Feeding Time" tune as the animals are trained to return to their cages when they listen to it.
MegaMan ventures into the comp restoring the lost programs to their respective places and coming to face the submarine Navi, DiveMan. The two battle and MegaMan succeeds in defeating DiveMan and activating the "Feeding Time" tune which returns the animals on their cages.
However, Captain Blackbeard takes Mick hostage in a last attempt to force Lan to reopen the cages and let the havoc continue. However Plata intelligently throws a beach ball close to Blackbeard. This causes the Elephant Seal, Fanny who loves her toy to rush for it and tackle down Blackbeard leaving him unconscious and to be arrested by the NetPolice.