To get rid of Magus, "Zeal" picks up the Masamune, hurts him and escapes with it. "Zeal"’s removal of the Masamune alters the timeline. (He wouldn't have bothered picking it up if the party and Magus hadn't intervened.) In the Middle Ages, things played out mostly the same in the early years of the Mystic War, except Cyrus was just a talented soldier, not "the legendary Hero". Chivalry and knighthood was less prevalent. Cyrus and Glenn die as ordinary soldiers and people quickly forget their names. Kasmir lives on to become a powerful Mystic illusionist instead of dying young. Without Frog's counsels and without the link to the honor code that the Masamune represented, the Guardians continued the war in 600 A.D. even after Magus's disappearance. The Mystics were forced to keep on fighting and were reunited by Kasmir, who became the new Mystic leader. In 605 A.D., a bewildered time-traveling Glenn returns from the CT Lavos quest and founds the Vanguard to try to restore peace quickly. However, the war drags on until about 650 A.D. (That's before Crono's party begins to interfere though.)
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This time around, Glenn is haunted with the feeling of having no place to call home. He has been "lost" ever since 590 A.D. when his friend Cyrus died (in the original timeline I mean) and he went into hiding in the wilderness as a mere frog-man. This repressed feeling was made worse after "Zeal" stole the Masamune in 11,995 B.C., as Glenn found himself in an alternate 600 A.D. in which Cyrus was never a hero and the Mystic War dragged on for decades, while people thinks he has delusional disorders due to his mumblings about the differences between his original timeline and this alternate, Masamune-less timeline...
Most people accept Glenn overall since he does create the Vanguard, but a few still think his mind isn't exactly sane. Without the King's protection, people would have thought he was crazy when he appeared out of nowhere in 600 A.D. talking about the war being over and Cyrus and him being heroes.
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In the original timeline, Kasmir was killed early in the war (probably by the Hero Cyrus) before he managed to develop his illusory spells. In the modified timeline, Cyrus died first and events changed so that Kasmir lived on and went on to become Magus's successor.
Kasmir knows a spell that allows him to create illusions of himself. Tons of battles happened between 600 and 605 A.D., but everytime Kasmir was defeated it was really just an illusion, while the real Kasmir has always remained safely hidden from the battlefields in his hidden fortress.
