I don't think anything outside the bold letters actually happened...
Yuji stopped Hecate from killing Shana, and then just left her in the Sereiden by herself while going along with Sydonay and Hecate to set up everything to SoF's comeback. Shana could awake the power of Alastor and scapped, following the Yuji's steps. There, the Master Throne is sacrificed to bring Snake to this world. Willhelmina joins Shana and they both fight Sydonay and Yuji. Shana eventually runs pass him and rescues Yoshida, she activates the Giralda and that's the end of the volume.
Shana and Yuji never got a single chance to kiss. Besides, if such a scene would happen, there would be for sure an illustrations of their first kiss, as always in light novels.
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