During level 9, the game briefly becomes a kind of shoot 'em up with players controlling a small, robotic drone to disable the security system of an oxygen facility.

A nuclear test conducted in 1995 by the United States of America government under the name Project Othello altered weather patterns worldwide, resulting in years of rain immersing the Earth in water.

Interstellar war broke out between a federation of earth's remaining governments and the Volarins, a group of extremists who seek to build an intergalactic empire.

The game's protagonist, a mercenary named John Cole, is hired by the federation through General Corbett to bring Nahj back alive.

He is assigned long-distance communication from his old friend Lieutenant Christine Mills: a technician with direct access to the federation's database.

After fighting hostile forces who attempt to destroy his transport ship, Cole arrives on Earth and begins his search at Omicron Station.

Local crime lord Quog points him to an energy station in the blue sector where an agent of the federation was found dead.

Sabotaging a supply depot and a sonar station, Cole arrives at the energy plant in blue sector; he finds the body of the agent who had liberated Nahj, killed with a shot to the back of the head.

Using the ion trail left by two missing power cells, Christine tells Cole that whoever took them has gone to an oxygen facility 300 miles to the northeast.

Christine tells Cole all files related to Project Othello were closed 20 years ago by General Corbett, then just a lieutenant.

The data files reveal Nahj's role in Project Othello was to develop nuclear bombs that leave no radioactive fallout.

Despite Nahj's warnings about side effects, the military forced him to speed up the test process resulting in Earth becoming Wetlands.

During the flight, Christine reveals Project Othello was never cancelled but placed on hold until the rains caused by the bomb tests ended.

After breaking through a squadron of Volarin fighters, Cole reaches Nahj's lead gunship, which contains a weapon capable of destroying planets.

However, he admitted that Wetlands is one of the better examples of the genre, since its traditional cel animation realistically models human movements, there are many good humorous touches, and the plot is more inventive and unpredictable than that of the more high-profile Star Wars: Rebel Assault II: The Hidden Empire, which was released at the same time.