Chrono Flux Plot

So, my plot had Magus from the original timeline grow old trying to rescue Schala only to get sucked into a time portal and dropped in the kingdom of Guardia at some point after the events of Chrono Trigger where Chrono had been transformed into a werewolf by the evil Masamune and Marle and their daughter had fled to safety.

Magus is asked by Guile to plumb the Dragon's tower where he frees Harle, who'd previously gone on the mission. They then head over to her home and are asked to find the cure for a form of petrification which is afflicting the locals. While doing so, Magus recognizes a statue as harkening from the time of Lavos and learns that a similar one showed up in Guardia just before Chrono went feral.

With his aid, they examine it but are captured by the invading armies of Parm, led by General Schala; who wants to recover the stolen Moon Stone. After breaking out of prison, they find the artifact and stop the war. Schala joins them and Magus learns she may be a version of his sister who was raised by the local magistrate.

Taking another conveyance to the Sea of Time, they encounter Glenn; who has been trapped here after crossing paths with Lavos in the future. The only way to free him is to climb a nearby tower and defeat the creature that waits at its top. But when they do so, Magus and his companions are thrust through a portal into an alternate reality.

On the far side, Magus becomes young Janus again. He's near to Parm and goes there looking for Schala but isn't able to find answers. Guile meets him and explains that Lavos has been manipulating the fractured reality in order to preserve himself. Upon returning to Guardia, they find it under attack by another version of Schala but are able to bring an end to this by producing the Moon Stone which Janus still has.

Afterwards, they go to see Glenn and he opens the way to the  Kingdom of Zeal which is now connected to this time line. Once there, they are able to convince the Queen that Dalton plans to betray her and using the Epoch; reach the Day of Lavos. Entering into the monster, they face Dalton but are unable to win. They gain the aid of Chrono's daughter and are able to cross over the two timelines at will.

In the end, the game had about 9 endings and lasted close to 10 hours for a regular run with additional content for multiple runs.
The resolution was that by harnessing the power of the Masamune along with an artifact they create, the timelines were able to be reconciled and eventually a happy ending was possible.
Oh and in this time line, Harle and Schala were dopplegangers from alternate realities where they were or weren't saved from the fire at Lucca's orphanage and part of the plot involved you traveling back to that day and having to choose which to save