For the second stage of the MSIP (Multi-Stage Improvement Plan), Boening upgraded the Phase 1 using lessons learnt from the Phoenix Initiative, resulting in the Phase 1's external transformation to the unique form of the Shiranui Second.
The head unit has been equipped with the newest active electronically scanned radar as well as an infrared target acquisition system. Thruster units were added to the shoulders to increase mobility, and the legs have been enlarged to increase propellant capacity. In response to the Soviet Su-37 Terminator, Boening quickly developed and installed thruster units for the Phase 2's waist blocks; unlike those on the Su-37, these waist thrusters are given vectoring nozzles. Improvements were made to speed up deployment of the combat dagger from the forearm sheath by several tenths of a second, and the TSF's Type-74 PB Blade from its Type-74 Mount Pylon by about one second.
Two units were produced for testing as part of Project PROMINENCE. The first unit, XFJ-01a, was initially painted in white and red demonstration colors during its unveiling and early combat exercises and assigned to US Army 2nd Lieutenant Yuuya Bridges. It was later repainted all white. The second machine, XFJ-01b, was painted in a dark-blue color scheme and would be piloted by 2nd Lieutenant Tarisa Manandal.
With the XFJ-01a, Yuuya would continue to test the machine in both JIVES tests and the subsequent Blue Flag exercises. Taking part in the first match of Blue Flag, Yuuya fought against the F-18E/Fs of COSEAN's Garuda Test Flight, managing to avoid their fire and overwhelm them.
In his second match, Yuuya and Argos Test Flight would face off against Bao-Feng Test Flight, with Yuuya scoring a decisive victory over UFC Lieutenant Cui Yifei's J-10X by maximizing the innate strengths of the Type-74 PB Blade that the XFJ-01 was equipped with; another contributing factor was his increased knowledge of the XFJ-01a's operation that was gained from his previous experiences. The XFJ-01b, piloted by Tarisa, would also experience its first combat action in this match.
While Yuuya's subsequent matches in Blue Flag would have eventually brought him against the Infinities, Yukon Base then came under attack by the RLF shortly after his victory over Bao-Feng. Both the XFJ-01a and XFJ-01b would be tested in live combat, with Yuuya and Tarisa in the XFJ-01a and XFJ-01b easily overpowering the terrorist-controlled automated F-16s; Yuuya also used the XFJ-01a to engage manned insurgent TSFs in combat. The XFJ-01s later fought against automated MiG-29s, the MiG-29OVTs of Major Christopher and his allies, and the BETA that had been released from underneath Yukon Base. The units then split their paths in order to stop the BETA; Yuuya and the XFJ-01a would team up with the F-22A EMD Phase units of US Army 2nd Lieutenants Leon Kuze and Sharon Heim, while the XFJ-01b, piloted by Tarisa, would engage BETA heading for the Red Shift line alongside Takamura Yui's Type-00F. The XFJ-01b was severely damaged when it encountered the berserk Scarlet Sisters, and the XFJ-01a itself was also damaged in the attempt to stop the Scarlet Sisters.
An attempt was later made by Yuuya Bridges to further upgrade the Shiranui Second Phase 2, but the blueprints were abandoned in favor of the upgrade plan for the Shiranui Second Phase 2 into its final Phase 3 form.
