The year is UC 0096 - 16 years after the One Year War and 3 years after the Second Neo Zeon War. A new conflict breaks out between the Federation and the Neo Zeon remnants over the possession of the mysterious "Laplace's Box", an artefact from the dawn of the Universal Century rumored to have the power to destroy the Federation. The seemingly ordinary schoolboy Banagher Links finds himself thrown into the middle of this conflict when he's chosen to pilot the Unicorn Gundam, which is not only a powerful mobile suit but also the key to Laplace's Box.
The year is U.C. 0096. Three years have passed since Neo Zeon and the Earth Federation Forces clashed in Char's Rebellion.
Banagher Links, a boy living at the manufacturing colony Industrial 7, meets a mysterious girl who calls herself Audrey Burne. Audrey claims that she is trying to stop the Vist Foundation from handing over Laplace's Box to the Neo Zeon remnants known as the Sleeves, an act which could spark another war, and Banagher decides to help her. But the colony becomes a battlefield as fighting breaks out between the Sleeves and the Earth Federation Forces, who have also come to stop the handover. As Banagher runs through the battle in search of Audrey, he has a fateful encounter with the white mobile suit Unicorn, which is the key to Laplace's Box.
With his dying breath, Cardeas, the head of the Vist Foundation, entrusted young Banagher Links with the Unicorn—the mobile suit which is the key to Laplace's Box. After battling the Sleeves pilot Marida Cruz and her Kshatriya, Banagher is captured by the Londo Bell assault landing ship Nahel Argama. Also aboard the ship are Banagher's friends Takuya and Micott, as well as Audrey Burne, the girl who contacted Cardeas in an attempt to prevent the transfer of the Box.
A single enemy mobile suit launches an attack on the Nahel Argama. This crimson mobile suit is the Sinanju, and at its controls is Full Frontal, leader of the Sleeves... the man who is said to be "the second coming of Char."
After launching in the Unicorn Gundam to protect Mineva, Banagher was captured in the middle of his duel with Full Frontal's Sinanju. He has now been taken to the resource satellite Palau, the stronghold of the Neo Zeon remnants known as the Sleeves, and placed under detention.
In order to recover Banagher and the Unicorn, Commander Daguza of the Federation's ECOAS special forces unit begins an attack on Palau, in coordination with the Nahel Argama. Banagher takes advantage of the confusion to escape Palau with the Unicorn, but...
Standing in his way are Marida and her Kshatriya, sent by Full Frontal in order to discover the path to Laplace's Box, which will be revealed by the activation of the NT-D system!
The conflict surrounding Laplace's Box has spread to Earth, and even the Earth Federation capital at Dakar is now suffering the terrors of war. Ronan Marcenas, a leader of the Federation government, contacts Londo Bell commander Bright Noa in order to prevent the opening of the Box.
Meanwhile, Banagher has landed on Earth, and is headed for the Torrington base where new information about the Box will be disclosed. But the fury of the Zeon remnants will drive Loni, the pilot of the mobile armor Shamblo, to turn the battle into a massacre.
Banagher is attacked by the black mobile suit Banshee, and taken into custody. Backed into a corner, he still continues to conceal the new coordinates leading to Laplace's Box which were revealed by the Unicorn Gundam. Bright, the commander of the Londo Bell, sees in Banagher the dignity and possibility shown by generations of Gundam pilots, and he finds help from old friends he once fought beside.
Meanwhile, Mineva has been handed over from Ronan to Martha, and she is transferred to the giant airlifter Garuda as a pawn to make Banagher talk. The conflict surrounding the Box soars to a high altitude and, finally, back into space...
Having escaped the pursuit of the Earth Federation fleet thanks to Full Frontal's intervention, the Nahel Argama is now forced to form a joint front with the Sleeves. Frontal, hoping to learn the next coordinates for Laplace's Box, reveals his secret plan against the Federation. Banagher and Mineva are horrified by the cruelty and callousness of the future he describes.
Meanwhile, a lone Federation patrol ship approaches the Nahel Argama. Will they destroy the patrol ship, or dissolve their joint front with the Sleeves? Caught between friend and foe, what choice will Banagher and his comrades make?
The location of Laplace's Box, which has the potential to overthrow the Earth Federation government, has finally been revealed. The place is Magallanica at Industrial 7, where the whole incident began.
Martha Vist Carbine, the acting head of the Vist Foundation, is determined to protect the Foundation's interests. Together with her nephew Albert Vist and Council on Colony Relations Chairman Ronan Marcenas, a central figure in the Earth Federation government, she heads directly for the Cheyenne base in order to resolve the situation.
Meanwhile, Banagher is hurrying to Industrial 7 in pursuit of Full Frontal, who has gone ahead to seize the Box. But standing in his way are Riddhe’s Banshee Norn and Angelo's Rozen Zulu.
Who will reach Magallanica where Syam, the guardian of the Box, is waiting?