Clouds is the story of Kita searching for her longtime companion, an alien known as an A'ahegre. The A'ahegre has been with Kita since birth and is one of the sources of her power and knowledge. The pair feeds off each other and grows more powerful as Kita's ambition has grown over the centuries.
The story also reveals the dark side of Kita's personality. Kita reveals her sociopathic tendencies and Cotton is unsure of how to handle this new revelation. Kita revels in her evil but is still careful to remain loyal to her friends. She knows one of her greatest strengths is her friends.
To find her A'ahegre Kita must find another A'ahegre who can tell her how to find A'a, the A'ahegre's homeworld. The problem is the cloud Kita finds is white and her's was black. They two types of A'ahegre have a conflicting philosophy and Kita must convince this white cloud to work with her, bringing back an old persona of hers, the Fallen Angel, the deliverer of judgment to the wicked and unrepentant. The white cloud provides Kita with the coordinates of an old A'ahegre ship that fled A'a.
Aboard the A'ahegre ship, Kita finds an ancient enemy of the A'ahegre, the Kiltrex. The Kiltrex are unlike any enemy Kita has ever faced. They're as advanced as Angels, making them hard to kill. Kita must fight through the ship to get to the navigational computer to acquire the coordinates of A'a.