In the paradox ending "Vanille's Truth", Serah and Noel are thrown back to the time after the War of Transgression after killing Caius in 200 AF Oerba. There, the two find Vanille and prepare to take her to Fang (as is common with the Paradox ending, it is an event that never really happened).
Snow departs on a journey intending to find Lightning. Eventually, he travels through time and becomes a Pulse l'Cie once again. Also, Lightning appears in one of his dreams, asking him to protect Cocoon's crystal pillar.
The Academy conducts the Proto fal'Cie Program with overlook done by Hope and Alyssa. The artificial intelligence malfunctions, kills the people in Augusta Tower, then creates machine duplicates of them as a cover-up for the incident.
In an alternate timeline, the Proto fal'Cie Program is abandoned after Hope sees an Oracle Drive where Serah, Mog, and Noel are fighting the Proto fal'Cie and Serah angrily shouts at him.
Hope and Alyssa sleep in a time capsule and wake up in Academia -4XX AF-.
A paradox occurs, resulting with thousands of flan merging into a giant flan in the Sunleth Waterscape that slowly melts the crystal pillar. Snow fights Royal Ripeness in order to protect Vanille and Fang residing within the pillar.
After resolving the anomaly, the number of flan drastically decreases with only some merging into a larger flan that was easily killed off.
Under the impression that their survival of the Augusta Tower in 200 AF to be a paradox, the Proto fal'Cie Adam creates Cie'th in order to eliminate Serah, Mog, and Noel prior to their arrival to that time period.
Many flan start to organize, with scientists dubbing this new behavior pattern "Flan Schools".
The old Cocoon falls, and the new one called "Bhunivelze", arises. Caius Ballad intervenes with the plan and attempts to crash the new Cocoon with the old one. However, Serah, Mog, Noel, and Lightning manage to stop him. Serah and Noel come back to Academia 500 AF after defeating Caius in Valhalla, but Serah sees a vision of the future and dies in Noel's arms. Lightning enters crystal stasis to preserve Serah's memory as the chaos of Valhalla is unleashed into the Visible Realm as a result of Etro's death, merging Valhalla with Gran Pulse and forming the world of Nova Chrysalia.