
Consulting his own diary, Sensei leads Naomi to slowly gain Ruri's affection and they eventually fall in love. On the night of the incident, Naomi refuses to invite her out for the festival and remains outside her house per Sensei's orders. They realise that due to this being a world within Alltale, Sensei's interference has caused its Homeostatic System to kick in. Bots in the form of kitsune men appear attempting to correct the data, transporting Ruri and Naomi to the site of the incident. Summoning a black hole, Naomi erases not only the kitsune men, but also the stroke of lightning that would have hit the tree Ruri was originally supposed to have waited at and hence the accident, successfully rescuing Ruri and rewriting the data.
In a twist of events, Sensei suddenly reclaims God's Hand and teleports Ruri away before disappearing. Naomi is shocked as he realizes that Sensei's plan was to recreate Ruri's original mental state in Alltale so that the data within could be synced with Ruri's own comatose mind in the real world, enabling her to wake up. Returning, defeated, to the city, Naomi is suddenly faced with thousands of kitsune men — an effect of Sensei deciding to reboot the system after all data relevant to Ruri's existence has been rewritten. The system then automatically starts filtering parts of data to keep and those to be erased, causing the space within 2027 Kyoto to shift and for red auroras to appear in the sky. Naomi, recalling how Ruri was teleported away in a similar fashion, jumps into the redness. He awakes in a virtual space to the yatagarasu, who assures him that he is not dead and promises to help him save Ruri, manifesting God's Hand for him once more.
Meanwhile, in the real world, Sensei embraces Ruri, who has woken up from a coma. However, kitsune men soon start appearing around the room targeting her, Sensei realized his world also a world within Alltale. Teenage Naomi warps to Ruri's hospital room and prepares to bring her to the staircase outside Alltale's complex, which has the optimal spatial coordinates for them to return to their original world. With help from Sensei, they manage to outrun the kitsune men and Ruri returns to her time via a portal created by God's Hand. The kitsune men, shifting their targets to the two Naomis, transform into a horrible gigantic creature that overpowers Naomi's strength. In the last moment, Sensei sacrifices himself, knowing that there can only be one Naomi and thanking his past self for letting him see Ruri smile again, wishing for him to always be happy. Inside the Alltale Management Facility, Alltale is successfully shut down after its data goes haywire and begins to duplicate itself. Alltale logic system has been deactivated which makes it possible to parallel world to happen inside Alltale. In tears, Naomi returns to Ruri and the two share a kiss. As the data has been written and rewritten beyond recognition, Naomi greets a parallel world ahead of him and Ruri.
In the final scene, adult Naomi awakens atop a human civilisation on the Moon, to the overlapping voice of the yatagarasu and an adult Ruri, implying that Naomi fell into a coma after saving Ruri due to the injuries from failing to enter Alltale in his previous attempts and now it was adult Ruri transferring Naomi's memory from Alltale to the real world.
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