Cosmic Era (C.E.) 71. Mankind has developed into two subspecies: Naturals, who reside on Earth, and Coordinators, genetically enhanced humans capable of withstanding the rigors of space who inhabit orbital colonies known as PLANTs. The story revolves around a young Coordinator named Kira Yamato, who becomes involved in the war between the two races after a neutral space colony secretly developing mobile suits for the Earth Alliance is attacked by the PLANTs' military force, ZAFT.

A young cartoonist intentionally gets near Ji Yan Xin, a cold and arrogant professor. Qi Nian, a girl with a straightforward personality hopes that interacting with Ji Yan Xin would give her inspiration and creative materials for her comic plot. Coincidentally Ji Yan Xin’s younger brother Ji Si Qi becomes Qi Nian’s assistant and a catalyst for their relationship to progress and blossom.

The Universal Century, a history marked by space colonization and space warfare, has passed. Humanity's prosperity, which ushered in a new era known as Regild Century (R.C.), was believed to endure alongside global peace. Bellri Zenam, a pilot in training of the Capitol Guard is somehow chosen by the G-Self - a highly maneuverable Mobile Suit of unknown origin - to lead to uncover hidden truths that will shake the peace of the Regild Century era.