Heero's Episode Zero takes place in AC 188. It backtracks and gives a brief scene of the original Heero Yuy's assassination in AC 175, and states that the assassin who killed him did not leave his name behind, but was a member of the OZ organization.
The story starts from there with Odin Lowe and a young boy. These two are headed to Colony X18999 to help with Colony Construction, and the boy is passing as Lowe's son. When they arrive at the colony, the boy stands staring out the window, and Lowe asks if he's staring at the void of space which took everything from him, or his own face in the window's reflection - a boy without a name. The boy does not reply; he merely asks why Odin Lowe came to the colony. Lowe responds that he plans to abandon the boy there, so the boy can settle down and live his life.
The boy is not impressed with this story, so he takes out a gun and demands to know who Odin Lowe is planning to kill. Lowe complies and tells him he's going to kill General Septum of the Alliance, and the boy should settle down and go to school. The boy replies that he'll do what he wants.
There's another backtrack to catch the reader up, informing us that on X18999 there were many uprisings in the past year by terrorists and rebels. These rebels were led by a man named Quinze. Septem was expecting backup to take care of the rebels, but this backup hasn't come yet. The Specials however, offer their services. Septem has never heard of the young officer named Treize leading these men, but he decides to let the Specials help.
On the front lines, Treize informs his men that actual combat is the best way to learn their training. He tells them not to fear, and to ignore the fact that they are outnumbered. Their strength is in their mobility. Since a lot of the communication sources are down, Treize states that he will be relying on a young cadet named Lucrezia to give him battle information. The girl requests that he call her by her last name, Noin, since all soldiers are equal and there is no gender on the battlefield. Treize agrees and the battle begins.
Odin Lowe is watching the battle with the young boy, and murmurs that a clever man must be in command. But the boy feels the rebels are no match for real soldiers, and they need a frontline command center. Odin Lowe chuckles that he's the sort of man for that job, and he turns to leave. But he gives the boy one bit of last advice - "No matter what happens, follow your feelings". He states that once, an idiot fired a single shot that changed history, and after that, Lowe left the OZ organization to live from day to day.
At that moment, two Alliance soldiers find Lowe and the boy, and Lowe takes care of one while the boy takes care of the other. Then Lowe tells the boy that no matter how careful you plan, someone will change the future. So it's best to live as your heart tells you so you won't regret it later, and the best path is to live in the present. With that, Lowe puts on one of the Alliance military suits, and the boy asks him to be careful because he's old now. Lowe merely replies, "Don't get killed".
The boy ends up running off into the battle on X18999, while Lowe goes to Septem. Right as Lowe fires, other officers take the bullets to protect Septem, and Septem orders Lowe killed. Lowe is wounded trying to escape.
On the battlefield, Quinze is realizing he's having problems against Treize's command. Dekim Barton orders Quinze to pull out of the mission because of his failure. Quinze is not a happy person. Treize orders his men not to attack Quinze's command vehicle. But even as Quinze leaves, a young boy appears with a missile weapon and opens fire on the Special's command tower. Lucrezia Noin reports that the boy is aiming at her, and Treize steps between to take the blow. Trieze is merely wounded, but he asks if Noin is alright. She shamefully replies that she is.
Septem makes a biting remark about the Specials, and demands his men find Odin Lowe. Lowe has escaped the Alliance soldiers and is bandaging his leg when Dekim Barton finds him and issues a fatal gunshot for revenge. Lowe realizes Dekim always meant to kill him, and the young boy arrives in time to talk to Lowe one last chance. He decides to get Lowe out, but Lowe tells him not to worry about that. Lowe asks the boy not to forget the few years they spent together, the years Lowe taught him assassination and spy work, and then dies.
The boy realizes Lowe left part of his job unfinished, and uses a detonation device to blow up a command center. Septem orders the Colony's weather control used to put out the fire.
Meanwhile, Treize is taken to the Barton Family Medical Center, where he meets a nurse named Leia Barton. She asks him to lie still, and Treize asks if it's raining. Leia tells him that the general order it so to put out a fire, and Treize mutters that Septem is an idiot. Leia agrees.
Nothing more is known of the boy who later calls himself Heero Yuy, but later he sees a man sitting in an alley. The man (Dr. J) declares that the boy has good eyes, and asks if he wants to become a Gundam pilot. Heero remembers Lowe's advice to follow your heart, and he agrees to become a pilot.