As an addition, since the dimensions all end up merging (according to the end of CC as I understand it); since they're most likely alive in the other dimension (and unless the merging of the dimensions killed EVERYONE from the other dimensions) then they would be alive in the resulting dimension anyway.
This is a point from Chrono Cross that I have always found confusing. There are times I wonder if Kato purposely left the ending this way so that it would be left up to the player to decide what really happened for himself. One thing that should be taken into consideration is when the time split happened in relation to Lynx's activities on the Zenan mainland. Although the topic is about Crono and Marle and their state of life after Porre overthrew Guardia, one thing that also needs to be taken into consideration is Lynx's role with Porre as well. That could lead to some insight as to what happens after the dimensions are re-merged.
Well, the sword may have been corrupted for a long time. It may have just been that enough negative energy and a dark possessed soul did not enter it ever before. The main things that probably stopped Frog from going wild was his oath to restore honor. But his whole situation seems like revenge, so the sword obviousally channeled that energy.
I dunno if it was Crono, any possibility is open, but whoever did it should be outside of time.
You'll have to define "long time". What discredits the whole idea that the Masamune was tainted during Chrono Trigger is that:
1) Crono, Marle, Lucca, and Robo had it in their possession before Frog ever claimed ownership of it.
2) Cyrus briefly possessed it. Furthermore, quotes from Frog's flashback indicate that Cyrus was sane while he used the Masamune.
3) Masa and Mune were conscious within the sword in Chrono Trigger, that is certain. It is not so certain in Chrono Cross due to these quotes from after you "free" the Masamune:
Radius:
I no longer sense the slightest
bit of malice from the Masamune.
There is no more fear of
succumbing to its enmity.
Mune:
Huaaah...
You awake, Masa?
Masa:
Yeah...
But looking back...
I think we've done
something terrible.
Mune:
Heh heh...
No one will know if
we don't tell.
Doreen:
HEY!
What were you
two up to!?
Masa:
Yikes!
It's Doreen!
Mune:
N-Nothing!
We don't remember a thing!
Doreen:
Hmmm, I see...
Well, just to make sure
you're not up to any mischief...
I'm coming along.
In Crono Cross Masa and Mune may have been lying dormant within the sword, and it is implied that they had no control over what happened to the sword. This is very different from Chrono Trigger, where they were conscious within the sword.
I do agree, however, that who or what tainted the Masamune could have been from outside of time. The question of who or what can't really be answered, and hopefully the next game in the series will answer it.
If people wish to speculate based on known information, it should be taken into consideration that the Masamune did disappear during 1005 A.D. From there, it was moved to El Nido. Based on known information, there are few possible candidates, if any, that could have tainted the sword or caused its disappearance. Furthermore, in 1005 A.D. the sword was still considered legendary, not infamous or demonic. Lynx did not exist yet, nor did the time split. The FATE computer, then, really had no reason to intervent on the mainland as of yet. It also appears unlikely that Magus would have been the one who tainted the Masamune. His life aim was always to exact revenge upon Lavos, and after that was completed, his only care was to find Schala (or was so implied). Furthermore, Lucca's letter discredits any other speculation of Magus' tainting of the Masamune, as she wrote that letter after the sword disappeared.