Actually, all parts of the game, except for one, point to the fact that each major decision creates an alternate universe based on the choices made and the most possible of outcomes, which was the pre-concept for Chrono Cross.
They tried to make it look as if it was direct effect and that you could change the events of time to change the future of the world, but that's not what resulted from it, as shown in Chrono Cross. The team thinks that's the case, but then the team in CC is shown differently. That may not have been intended until after CT, which would make the point moot, but I'd like to think that they did think of that back then.
If we assume that they did, then it leads to the subtle insinuation that there is a very powerful 'entity' that pulls people strings like puppets and changes things as it sees fit to avoid certain cataclysmic events. This IS hinted at in the original CT, which lends credit to the idea. If this is the case, then events like Marle disappearing in 600 AD as direct co-relation to Leene's disappearance would absolutely be attributed to this 'entity', as it would not occur with alternate timelines.
Let's move over to FF8's time disruption for a moment. It also deals with alternate realities based on decisions and possible outcomes, though you don't see too much of that in the game. They deal with one linear timeline that loops into itself, cutting all involved off from outside interference, as evidence when *spoiler* Squall goes back in time to the Orphanage and gives Edea the idea for Garden and SeeD, which raised a very important question: Who actually came up with these ideas?
straight answer: we don't know, but we think that somebody outside of the loop had to have done so at some point to be able to initiate the loop. That's if we assume that time is linear and that there is a definitive starting point to time at some point in the history of the cosmos, which is quite a stretch, if you ask me. You have Edea starting Garden and SeeD with Cid and their first students are the kids from the orphanage, those that weren't adopted. Those kids are raised knowing absolutely nothing about the Sorceress or the future threat that comes from them. They learn all of this on their quest to liberate Timber.
But, if we assume that time is not linear, then the whole loop has to be viewed as a whole. It meanders a bit, some times going in a straight line, some times doubling back on itself, some times traveling sideways. Our minds are what give linear viewability to what we intake, to make sense of things.
Let's further think of 'time' as an advanced code. First thing you do when you create a code is troubleshoot; you look for bugs, etc., but you fine tune until you come the closest you can to perfection. You beta test, you alpha test, you throw free products out to people until you can finally code it near enough to perfection to be indecipherable from perfection except to those with keen sensibility. Would we then assume that our very cosmos in its seeming perfection is allowed to have such bugs as 'paradox' in it? Would we then assume that there's not several various levels to the world like some MMO's have various layers for their players when one layer gets over-crowded, or to allow for multiple parties to go through the same motions at the same time in their own ways and methods without interfering with each other?
My point is this: with time not being linear and with multiple layers of it, there is an endless amount of alternate dimensions that are all existing alongside each other and top of each other and in and through each other, allowing for time travel and allowing for things that would cause paradox, but not allowing them to actually cause paradox. Of course, there is always the idea that what happens through time travel was always meant to happen and thus the future is changed already to suit it and anything we do by going to the past would already have been done and we're just performing to what was already done.
But, back to Marle, we have to assume that the CT crew utilized the Alternate Timeline Theory, allowing for multiple dimensions to overlap each other and to exist simultaneously; due to the storyline continued in CC. We further have to assume that an entity is at work far beyond the scope of Lavos and our heroes as evidence in both CT and CC; and that they meant to give us the illusion that we were changing the present and future in CT instead of just forging a new path altogether. We can assume these things by the elements in the game and their misleading natures.
What this means is that they can do anything they want with the heroes of these games and still bring them back for a sequel.
