MS igLoo 2 goes back to the first MS igLoo and tells the story of the Federation soldiers side that has to fight against the monstrous Zakus. Each episode tells a story of a different federation soldier that is cursed by a Death God that came down to earth with the Zakus and shows the desperate struggle against mobile suits with only conventional weapons such as tanks and missiles. Each soldier, fueled with revenge, and a Death God looming over their backs, fights against the odds that is the terrible might of a Zaku.

Ensign Shiro Amada is transferred to Southeast Asia to take command of the 08th MS Team. In their first guerilla operation, Shiro's team is tasked with distracting the Zeon forces while Federation ground troops locate a mysterious new Zeon weapon.

Advanced Generation (A.G.) 101. The space colony Angel is attacked and destroyed by a mysterious "Unknown Enemy" with overwhelming strength. As this "UE" continues its attacks, a boy named Flit Asuno loses his mother when she is caught in the crossfire. Now in A.G. 115, Flit must fight using a new Gundam of his own creation, which evolves itself through battle. The curtain rises on an epic Gundam saga spanning 100 years and three generations.

After Colony (A.C.) 195. Mankind has moved into space. Thousands of people live on giant orbiting space colonies called "Sides." However, the Earth Government, which rules the colonies, is unjust and cruel. A group of revolutionaries builds five robotic weapons called Gundams and plans to send them to Earth to begin their fight for independence. Piloted by five young men, these Gundams carry the hopes and dreams of freedom of the colonists with them as they descend to Earth to begin Operation Meteor!

When Banagher Links meets the mysterious Audrey Burne, he inherits the Unicorn Gundam and is swept up into the battle for space colony independence.

High-school student Amate Yuzuriha lives peacefully in a space colony floating in outer space. But when she meets a war refugee named Nyaan, Amate is drawn into the illegal mobile suit dueling sport known as Clan Battle.

Cosmic Era 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.

It is the Universal Century, year 0153. The Zanscare Empire, which rules almost all of Side 2, has declared its independence from the old government, the hollow and corrupt Earth Federation. Under the justification of creating a new, space-based order, it has begun an invasion of Earth; and Point Kasarelia, the illegal residence area in Eastern Europe where Üso Ewin and Shahkti Kareen live, is no exception. As they are caught in the fighting between Zanscare and the opposing resistance organization, the League Militaire, fate draws Üso and his friends into the midst of battle.

U.C. 0097, one year after the opening of "Laplace's Box". Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix… named Phenex.

Universal Century 0079. The One Year War rages on, and Shiro Amada and his unit, the 08th MS team, continue their struggle against Zeon forces in the jungles of Southeast Asia. But recent events have put them under close scrutiny by Federation leaders. Alice Miller, an officer of the Federation Intelligence Division, has been dispatched to ascertain the truth behind a series of events leading to the capture of a new enemy mobile armor. As she begins her investigation, the lines between Federation and Zeon become blurred. Is there really a spy among the 08th MS team?