During the Armory One Incident, Lunamaria, along with Shinn and Rey, is drawn into the conflict, but the stolen units escape and are picked up by the mirage colloid–cloaked Earth Alliance battleship Girty Lue, waiting outside the colony. The Minerva pursues the Girty Lue, engaging in several battles.
During the pursuit, Lunamaria meets former ZAFT member Athrun Zala, who is using the alias "Alex Dino" and acting as Cagalli Yula Athha’s bodyguard. Lunamaria's interest in Athrun grows when he re-enlists in ZAFT as a member of FAITH and joins the crew of the Minerva. Her attempts to get closer to Athrun are sometimes thwarted by Lacus Clyne impersonator, Meer Campbell. Ironically, Lunamaria appears not to notice her own sister Meyrin's interest in Athrun, even when the two discuss him.
Later, Talia Gladys, captain of the Minerva, orders her to spy on Athrun when he meets with his former comrades Kira Yamato and Cagalli from the Archangel. During this meeting, Lunamaria discovers that the Lacus she knows is an impostor. She gives the data and photographs she collected to Talia, but omits mentioning that the Lacus Clyne working for PLANT is not the true Lacus. There are times when she appears to want to discuss the matter with Shinn, but she would not when Rey is around.
The Minerva participates in several incidents during the Second Bloody Valentine War. During the Battle of Crete, Lunamaria’s ZAKU Warrior is heavily damaged and she is badly wounded. Upon the Minerva's arrival at Gibraltar, Lunamaria has recovered and replaces Shinn as pilot of the ZGMF-X56S Impulse, since he is now piloting the ZGMF-X42S Destiny.
Lunamaria is shocked when she is informed that Athrun and her sister Meyrin have defected together and that Shinn has destroyed the GOUF Ignited in which the pair had attempted to escape. In grief and denial, Lunamaria places the blame on Logos rather than Shinn, who is clearly upset over killing her sister. Lunamaria and Shinn begin relying on each other for emotional support and develop a romantic relationship.
After Operation: Fury, Lunamaria discovers that both Athrun and Meyrin are alive and on the rogue battleship, Archangel. At the Battle of Messiah, Lunamaria refrains from attacking the Eternal, when she discovers Meyrin is on that ship.
Lunamaria then battles Athrun, blaming him for taking her sister Meyrin away. He badly damages Lunamaria's mobile suit, the Impulse, with his ZGMF-X19A Infinite Justice. Because Lunamaria is getting beaten, Shinn enters SEED Mode and attacks Athrun with his ZGMF-X42S Destiny. Lunamaria interposes herself between the two, trying to get them to stop fighting. Shinn is too enraged to understand what Lunamaria has done, but Athrun enters SEED Mode, blocks Shinn's attack, and saves Lunamaria. Athrun then cripples Shinn's mobile suit and Shinn crashes on the surface of the moon. Lunamaria lands her damaged Impulse nearby and ends up holding a tearful Shinn in her arms, as they watch the Requiem superweapon explode and then the ZAFT fortress, Messiah, crash into the Moon.
In Gundam SEED Destiny "Final Plus", both stranded pilots are later rescued by Athrun Zala in the Infinite Justice. At the end of "Final Plus", Lunamaria is present with Shinn (alongside Athrun and Meyrin, Kira and Lacus) as he pays tribute to his deceased family in Orb.