Following its return, the Earth Federation Forces Clop-class Damascus was deployed as part of the "Phoenix Hunt" taskforce at the request of the Intelligence Bureau to capture the Phenex. With the intervention of Jona Basta and the RX-9/A Narrative Gundam A-Packs, the operation almost succeeded, but Jona allowed it to escape. The Phenex reappeared to assist Jona and his RX-9/B Narrative Gundam B-Packs in the battle against Zoltan Akkanen and the MSN-06S-2 Sinanju Stein at the Metis Colony in New Side 6, before fleeing the colony at near-light speed. During the final battle against the NZ-999 II Neo Zeong at the Helium-3 storage base, Jona entered the Phenex's cockpit after escaping the destruction of his RX-9/C Narrative Gundam C-Packs using the Narrative's core fighter.

With Jona at the controls, the Phenex activated its NT-D System, transforming into Destroy Mode and swiftly defeated the II Neo Zeong and Sinanju Stein. However, Zoltan's death released psychic energy that caused all the nearby Helium-3 storage tanks to reach critical. Thankfully, the Phenex was able to utilize the pieces of psycho-frame scattered earlier by Michele Luio and Brick Teclato to generate a pair of wings with its Armed Armor DEs to reverse the explosion and make the II Neo Zeong and Sinanju Stein vanish. With its task complete, the Phenex sped away in Destroy Mode to parts unknown, leaving Jona behind with Banagher Links who noted that even moving at light speed would not be enough to catch up with it.