Warning: spoilers ahead. The spoiler statute of limitations should be long since past on this one, though.
A significant amount of the plot in the first half of Chrono Trigger revolves around the war between Magus's armies and the kingdom of Guardia in the Middle Ages.
Later on, you find out that Magus is actually a grown-up Janus, who as a child was displaced in time following a disastrous attempt by Zeal to summon Lavos, and his chief motivation is to re-summon Lavos and destroy it in order to get revenge.
This raises the question, why is Magus at war with Guardia in the first place? This doesn't appear to have anything to do with his goal of summoning Lavos, and could only have served as a distraction from that goal. Furthermore, his actions in the conflict, particularly when he went to deal with Cyrus in person, ended up being actively counterproductive to that goal by inspiring Glenn to take up the Masamune and hunt Magus down.
Do we have any reason for why the war was going on in the first place?