I've came up with a few ideas for Chrono Brake.
The Frozen Flame would return, however, not just one - multiple Frozen Flames. Being defeated twice, Lavos' desire for ultimate destruction has caused him to split a large portion of himself into several Frozen Flames across time periods. Each Frozen Flame (maybe 5 or so) in different time periods has an effect on the future, thereby causing multiple dimension splits. This is where the "Chrono Brake" comes in. The Chrono Brake would be able to simultaneously stop all of the split timelines and converge them together into one complete timeline, with no effects from the influence of Lavos and the Frozen Flames. However, like in Cross, in order for this to be accomplished Lavos must be defeated yet again. Lavos' plan this time is to call back all the arbiters and accompanying Frozen Flames to him. He's pulling out all the stops, putting all of his remaining energy into the brainwashing effects of the Frozen Flames, thereby enslaving all arbiters to the will of Lavos. The characters must travel across each time period/dimension where the Frozen Flame is having a negative effect on the timeline and defeat each arbiter from wreacking havoc on the timeline. Once all arbiters are defeated, their ultimate goal is discovered - to find their way to the Darkness Beyond Time and perform the ultimate fusion with Lavos - to become the Planet Devourer.
It needs refining but I thought I'd throw my ideas out there. Opinions?