Retiring as a soldier of the government of a high-tech city, Fay Ryu Kazuhiko's transition into civilian life is cut short when his superior, General Ko, summons him. Having a leaf imprinted onto his hand by code, Kazuhiko is entrusted with a secret task to deliver a "package"—a girl with white hair and evergreen eyes whom he finds singing in a birdcage-like building. All Kazuhiko knows is that her name is Suu, and for whatever reason, she wishes to go to Fairy Park.

As his friends Lan and Gingetsu help set up a transport module for the duo, Kazuhiko suspects that there is more to Suu than he knows. Not only is their transport intercepted, but the two are also pursued by Bols—a face that is uncomfortably familiar to Kazuhiko and who seems to have received his own mission to seek out Suu. The truth behind the discreet nature of this operation, Suu's existence, and even a possible connection between her and Kazuhiko may all be linked to just one word: clover.

Clover was published in English by Tokyopop from May 15, 2001 to March 20, 2002 before the company went defunct. The license was then acquired by Dark Horse, who released the title in one complete omnibus volume on May 13, 2009 as well as digitally on May 21, 2014. Kodansha Comics USA later republished all four volumes as one omnibus volume digitally on June 30, 2020 and in print on September 8, 2020.

The series has also been released in French by Pika Édition from July 18, 2000 to November 12, 2001 and in German by Carlsen Verlag.