After Colony 205, ten years after the incidents at colony X-18999, the second attempt at Operation Meteor by the Barton Foundation and the death of Mariemaia Kushrenada, the Gundampilots have forever lost sight of 1 another and all assumes that they've moved on.

Peace has returned to the space colonies and planet earth and a golden age has begun for mankind. But is peace really meant to last for all eternity??

While attending an annual charity ball, president Relena Darlian gets shot. She fights the wounds for hours and hours but in the end she dies in the hospital but not alone. Besides her bed appeared a gloomy man, sitting next to her and weeping as they say goodbye.

"I shall avenge your death Relena, even if it's the last thing I'll do ..."

As the nurse walks into Relena's room, the man pushes her out of his way and quickly runs towards the exit, on to the parking lot where he gets into a black sports car and drives off ...

For weeks nobody claims responsibility for the assassination of Relena Darlian but the vice-president, Yusuke Tsunami, fears that her assassination was only the beginning of something far greater and begins to reconstruct factories to create mobile suits. After Yusuke is appointed as the new president, he reastablishes the military and law enforcement agencies.

The time of peace has clearly ended and people are turning against the current government and it's new policies about warfare. In the midst of all this misery, a man comes forth and tries to convince people that civil war is not what they need and suggest that they form separate governments and countries to prevent war. The man identifies himself as Zechs Merquise, the war hero who had not been seen for ages, and is appointed as leader of the new military force Omega.

Five years later the world has completely changed and the golden age has been all but forgotten. Mobile Suits are often seen, patrolling the area, either on land, in the air or in the water. The old military bases which were located in outer space have also been repaired and several new ones have been added to the number. People have begun to live in fear of what might happen if the new nations would start a war, or if one of the colonies would attack planet earth once more. It's in this period that a previously unknown organisation called Akuma begins to randomly attack some countries and also claims responsibility for the death of the late president Relena Darlian. Immediately Zechs Merquise orders Omega to move in on the enemy and creates a new organisation, Treize, which will serve as military intelligence in order to locate the enemies base of operations and the people in charge of Akuma and where they are hiding. But they can't seem to find any trace what so ever of their new enemy and have to rely on their defences to hold the forces of Akuma back. President Tsunami declares the state of emergency and pumps more funds into military intelligence and gives his war factories more money to develop new and better weapons in order to protect the nation's borders. Meanwhile in outer space, several of the colonies have been invaded by Akuma and the new lunar base has been destroyed. The people once again turn to their governments with angry words and hostility but this time Zechs can't convince them with words so instead he places several individuals under arrest. He is now fighting two enemies, foreign and domestic, the forces of Akuma and the hostile civilians who have gone underground and started a wave of terrorism.

After Colony 215, Zechs Merquise has taken command of all military forces and the government when former president Yususke Tsunami was murdered by the underground resistance. In space, a man has taken control over all of the military bases and begun the construction of an improved lunar base. Not much is known about him and he never shows his face, all those who gaze upon him end up dead. Though he has not show any hostility towards Omega or Treize, he has taken over some of their outposts and convinced their soldiers to aid him in his goal; to destroy Akuma and it's leader. Zechs no longer stand alone in his war ...

After Colony 217, October 12th, Akuma has retreated to planet earth and several outposts in outer space, Zechs and Omega and Treize have left their home planet and retreated to colony X-25666 where they were welcomed by their allies. On arrival they see an incoming ship and Zechs sees someone he knows from the past, a tall young man with little or no expression on his face. The young man ignores the soldiers and disappears, leaving his cargo in the main dock.

Zechs and his man are told not to move through a certain area of the colony and Zechs is requested to join a meeting of the colony's leaders who have planned the final attack on the forces of Akuma and mean to reclaim planet earth ...

After Colony 217, October 13th, Zechs is accompanied to the meeting by two bodyguards in service of the colony's leader. They escort him to the restricted area where he can only see military activity and lots of factories which are used to build mobile suits of all sorts. When they reach a large wooden door, the bodyguards tell Zechs to enter and then keep watch at the door. Upon entering the room, Zechs quickly discerns three very familiar faces from his past; Trowa Barton, Duo Maxwell and Chang Wufei, the former Gundampilots and lady Une.

It seems that Trowa Barton found some old soldiers of the Treize Fraction and convinced them to help them in his fight against Akuma in outer space and they quickly gained the upper hand. Trowa then send several soucts to try and locate his former comrades, his brothers in arms, the Gundampilots; Heero Yuy, Duo Maxwell, Chang Wufei and Quatre Raberba Winner. Only two of them were present today, Duo and Chang. Apparentely Quatre was working on something which had been kept secret. They had begun to construct not only mobile dolls but they had also just finished building several Gundams ...

Heero Yuy was the only one who the scouts could not find, until a spy infiltrated into Akuma and managed to take a picture of it's leader; Heero Yuy ...

During the meeting the plan was made clear, Trowa, Duo, Chang and lady Une would lead thousands of mobile suits and infantry into battle against Akuma an it's forces and try to figure out why Heero would've killed Relena ...