Far future, since I don't know that much about the early games lore and I didn't play SoV. The historical Marth and Alm, after doing the things they're famous for in-universe, then suddenly disappeared. They were still in the prime of their youth (thus fighting ability), but nobody knew what happened to them. I think you can guess where I'm going with this.
Let's set it after Awakening. The League of Nations (the continent of Ylisse) is at odds with the Valmese Empire. Neither wants a war but instead they mistrust each other and this is an obstacle to peace.
On the day of a major festival to Naga, observed across the Ylissean continent, a date which coincides with a diplomatic conference between kings in the continent's heart, Valm suddenly launches a full-blown invasion with zero warning. The most formidable Valmese general is Alm in the flesh, who reappeared in the vicinity of the Valmese imperial court about a year ago. Marth, who also reappeared a year ago, shows up and helps the League defend itself.
As it turns out, this is not the first timeline. Alm came here from a previous timeline where it was the League that invaded first, and after traveling back he convinced Valm to launch a preemptive strike to protect the continent's people.
They fight for a while, and a butt ton of people die, but then both sides realize they're being set up. There is another country far away, whose people are devoted to an evil dragon god who can manipulate time. He is the one who brought Marth and Alm here. He brings a bunch of baddies ("earth dragons", I guess) from the past, who had narrowly escaped death before vanishing, to help him take over the present. Bad guy believes both sides have weakened each other sufficiently that victory is now possible.
Final showdown, where Marth, Alm, and MC team up, and they save the world. Credits roll.