The children do not hear from Tai and Agumon, who stayed behind to take on Machinedramon. The children are in deep sorrow. Meanwhile, Millenniummon’s body is gradually being prepared for the resurrection.
After Tai and WarGreymon's apparent demise with Machinedramon's power cores, the Cloud Continent becomes covered in miasma and darkness, noticed from ElDradimon by Leomon and Lopmon. At that point, FAGA emerges from underwater with the Vademon and Sakkakumon. Absorbing the black lightning created by the miasma, Sakkakumon begins to digivolve into a white Kimeramon. With Mimi and Joe staying behind to protect Kari and T.K., Matt heads to engage the Vademon with Sora and Izzy. However, a Gryphonmon is summoned by Kimeramon to keep Matt and MetalGarurumon busy, leaving Garudamon and MegaKabuterimon to deal with the Vademon. They manage to score a hit on the still digivolving Kimeramon, but the smoke clears to show its digivolution complete, before it starts to be absorbed by FAGA to complete Millenniummon's rebirth. In the meantime, MetalGarurumon finally destroys Gryphonmon and moves to assist Sora and Izzy, but their attacks have no effect on FAGA.
Watching from the ground, Mimi does her best to encourage Kari to maintain hope and faith that Tai and WarGreymon are alright. With Mimi's help, the two girls are able to make corsages to give to Tai and Agumon when they come back safely.
However, in the end, Kimeramon is absorbed by FAGA, and with the Vademon willingly allowing themselves to be destroyed with their duties as Millenniummon's followers complete, Millenniummon is reborn. However, it is revealed that WarGreymon is still alive as he emerges from a pillar of flames, but as he does, Kari, Joe, T.K., Mimi, and their partners appear to vanish from the purple energy being released by Millenniummon.
(Numbers indicate order of appearance. Bolded characters are fought by the protagonist(s), and italicized characters feature non-explicitly, e.g. voice, silhouette, image.)