This takes place both after the end of Bluseed and the end of Chrono Trigger (an excellent PS1 game if you didn't know)
Kaede's kushenata soul is used to revive Lavos into the flow of time itself, causing it to unravel and ages to start overlapping. Kusanagi and Momiji discover one of Lavos' portals to which Lavos and Kaede walk out of. A battle insues causing Momiji to die and Kusanagi to follow into Lavos' portal after him.
Cut to the chrono gang -
Janus' Castle appears in the 1000AD times and he seeks help from Chrono, Marle, and Lucca to get to the end of time. They speak with the elder at the end of time and he tells them that in order to lock the flow of time from distorting itself further they must seal it at the beginning, middle, and end of time. So the four split up and go to the other eras of time to seek help from their past and future friends.
Kusanagi appears in a desolate future of a destroyed Tokyo. Glenn works with him to help him survive in the era. With the help of the great Melchoir, they travel to the end of time and learn of their friends mission. Kusanagi joins the group in their mission to fix the flow of time.
Lucca, going to the destoryed again futuire searches for Robo, Magus to the middle ages to find his servant Ozzy, Chrono to the past to find aid from Ayla, and Marle to get help from her ancestors. The pace of time unraveling increases and events become distorted. Existance starts to fade and people dissapear.
So, the network of the ages must work together to lock the flow of time, discover the mystery of the Kushenata, stop Lavos and Kaede, and protect the future of all.
(I know this story includes several characters, but several will be inactive after the first few chapters due to an event I cant divulge
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