As the space-borne rebels called White Fang rose to power, Heero attempted to assassinate Relena, who had become Romefeller's chief representative and Queen. However, after Relena's speech about her plans to change Romefeller into a peaceful World Nation was met with positive feedback, Heero chose to spare Relena and give her the chance to do so. Heero then headed back to space with Sally Po and met up with Peacemillion, the spaceship designed by the Gundam engineers. Having achieved mastery of the ZERO System, Heero loaned Wing Zero out to Wufei and Trowa, giving the former the conviction to join the other Gundam pilots and restoring the latter's memories when the two of them utilized the ZERO System. When White Fang began using the ZERO System to coordinate its mobile doll forces, Heero had a portion of the ZERO System copied and installed into Quatre's Gundam Sandrock, enhancing his leadership skills with the system's abilities.

After Duo learned that Relena was being held prisoner on White Fang's space station Libra, Heero infiltrated the ship to rescue her. The two encountered Zechs, but were unable to convince him to stop his plans. As he prepared to head into the final battle, Heero promised Relena that he would live through the war, and return to her. Heero immediately went after Zechs, and the two engaged in a duel that spanned Libra's airspace and the station's interior. Though both Gundams received heavy damage, Heero came out on top. As word of the peace agreement came to them, Heero was given the opportunity to finish off Zechs once and for all but didn't out of respect for Relena. With that, he left Zechs to destroy Libra's main power system. Unfortunately, Libra had been set on a collision course with Earth. And worse, Wing Zero was out of ammunition and energy, so Heero chose to once again self-detonate his Gundam. But before he could push the detonator, Zechs came down, admitting that someone who is strong and pure can empathize with people, like Heero. Therefore, Zechs used Epyon to sacrifice himself in order to destroy the power core, though he promised Heero that they would meet again.

But even with Zechs' sacrifice, a portion of the Libra block was still descending towards Earth, with the capacity to cause a never ending winter on the planet. Flying into the upper atmosphere, Heero used Wing Zero's buster rifle , which Wufei had returned to him at only 30% capacity, to destroy the massive falling section of the Libra. This was a significant event for another reason besides the fate of the Earth.
During the war, Heero did not care whether he lived or died; he only cared about the mission at hand. However, while he was descending into the atmosphere with Wing Zero's buster rifle pointed at the Libra, he proclaimed that he will survive. This shows that his time with Relena had given him a will to live and something to protect.

Following the war the members of STARWOLF vanished from existence though they had aided the G Team during the war after discovering their origins and the blueprints of their Gundams from the computer of Doc J they are clones of Heero Yuy.
Liquid Wolf then asks his twin " so we are not meant to exist ? "
Solidus Wolf then responds putting a hand on his brother " in a way yes but it still doesn't change the fact that we are born for a reason and it will seem that this is that reason to safeguard Heero in that since it will make him our father , but do not tell him that we are clones or he is our father. I don't think he can handle it. He may be a soldier but he is still only 15.
We should just keep our distance from him and should we be forced to work with him to only use our codename then our real name unless he asks us. "
Solid Wolf turns to his brother and twin telling them "We can tell other people about having faith. What we had faith in. What we found important enough to fight for. It's not whether you were right or wrong, but how much faith you were willing to have, that decides the future."

" What should we do with our Gundams then , if we want to stay away from the rest of the G Team our Mobile Suits are apparently next gen models using a Ultracompact Nuclear Fission Reactor , destroying them here will be destructive ? " asks Liquid.
" We will keep it in the case wars break out again , I also agree with my father working with him and the rest of the Gundam pilots has given them something to protect , peace. " responds Solid " wars are so easy to start and so hard to end. "

STARWOLF had decided to disband from the G Team and naming themselves Cerberus and becoming Mercenaries finding their calling on the battlefield spending most of their life there and not knowing any other path.

In the summer of A.C. 196, Heero and Duo decided to help Relena's movement towards total disarmament. While she investigated former weapons manufacturers, the two pilots sneaked into their bases, searching for hidden mobile suit construction lines. However, with the notion that OZ's lost mobile doll plant might not be a rumor, Heero decided to investigate it further. His first act was to speak to Dorothy Catalonia who, as the granddaughter of Romefeller's chief representative, would be privy to any such knowledge. Initially, Dorothy coyly pretended not to know anything and offered to let Heero spend the night at her mansion. The next morning, she revealed that she had invited Relena along, hoping to spark a romantic meeting. However, both Heero and Relena were more concerned with Vulkanus, so Dorothy gave them the only information she had on it and allowed them the use of her database. While they worked, Relena offered Heero a position with Preventer, but he declined, citing his desire to work alone. Eventually, they managed to discover Vulkanus' orbit, and with Relena's help, Heero returned to space. Using Wing Zero's high-speed booster to catch up with the other pilots, Heero arrived just in time to help them fight off the Perfect Peace People and the Scorpio suit. Wing Zero dealt the finishing blow to the Scorpio, and when Quatre proposed his idea of destroying the Gundams by sending them to the sun, Heero agreed.

On Christmas Eve, December 24, A.C. 196, Quatre carried out the plan to destroy the Gundams by sending them, with Vulkanus, into the sun. All except for Wufei's Altron Gundam were sent. In the meantime, Heero continued to look out for Relena from the shadows. His investigation into the colony L3 X-18999 quickly let him learn that she had been captured, and he enlisted Duo's aid in a rescue attempt with Cerberus watching from the distance.
The mission has brought about a bit of concern in Duo who normally deeply cares for his comrades and is never afraid to rush to their aide in battle.
Heero reassures his friend " do not worry , I have contracts on standby all I have to do is give them the code name and they will start their mission should anything happen to us if you remember STARWOLF. "
" Oh them but why will they help us ? " Duo then asks
" Duo , I will save that for another time "