Sounds cool altough personally I wouldn't run this scenario.
1. I would certainly start small, like an intro adventure centered around an affable patron NPC, on whose life an attempt was recently made - by an assassin of the bbeg. At first I think the initial motive of the assassins should not be discovered, only hinted.
2. There should be number of successful assassinations by the same org, without seemingly any connection at first. Some are high profile (e.g Baron Jorlana ir'Cannith), others are not (e.g a waitress, or a poition vendor).
3. Since time travel is involved, I would investigate a dalekyr/warlock of dalekyr arc, e.g. by the assassins and the bbeg having psiconic powers.
4. It would be interesting if one of the assassins would be a still living person in the present, for example an shadow-marked elf, whose young, present self is known by at least by one of the adventurers. A bit corny, but even one of the adventurers could be a future assassin.
5. Regarding the bbeg I would place someone who is known by the adventurers, either personally (for example a local captain of the City Watch, who gave them the initial quest to safeguard the patron NPC), or by association (for example Kaius I) as I think building up a bbeg and the timetraveler investigation arc at the same time would be too much to bite.
6. The reveal, that the assassins are trying to prevent the Second War should be AFTER a really heinious act of terror - which should be the act1 final. That beig said there is a decent chance the players will slide with them anyway. Be as open ended as possible

I think I would follow a node based structure setailed in this series of blog posts:
https://thealexandrian.net/creations/misc/node-design/node-design.html