This is from the other thread I responded to but i'll bold the part that pertains more to this question....
"He (Magus) ignores this purpose for decades to fight a war between Mystics and Humans."
So on this first point I would say that because we don't fully see Magus' story line playing out in these years that it's difficult to say one way or another what his motives were. However, I would argue that Magus eventually would have figured out that Lavos fed off of division and destruction (In Magus' time (10000BC) as a child there were two different classes of people (magic and non-magic) and as Magus grew older in 600 AD he may have come to realize that that division between his people who could use magic and could not was actually created by Lavos itself (this is confirmed later by Schala when you are in 10000BC and she says the folks who can use magic are posssesed by Lavos)).
What i'm getting at here is Magus started to war to summon Lavos. He was purposefully trying to create division knowing it would summon Lavos which it eventually does at the worst possible time for Magus.
"He also makes no attempt to avert the threat or save anybody when he is the Prophet in Zeal."
This isn't exactly true depending on how you look at it because when he discovers Chrono and the gang in 10000BC he tries to send them back to their time and has Schala freeze the time seal. Older Magus may understand that as a Child he witnessed Chrono sacrifice himself with Lumainaire to save everyone when Lavos appears and resists the Phophet's attack - this "event" is what causes everyone, including Magus, to be warped to different points in time and results in Schala's death - it's this event Magus is trying to stop.
I believe that it was Magus' belief that by freezing the time portal with Schala that Chrono and his gang would be locked out of 10000BC and that "the event" he witnessed as a child would not happen thus giving him, Magus/Prophet, the sole chance to defeat Lavos after his sister raises him without anyone interfering. Magus' flaw is believing he's powerful enough to stop Lavos by himself.
It's my interpretation that Magus' plan was to get rid of Chrono and his gang (he starts immediately by telling the Queen they are coming) because he believes if he gets rid of them then he and he alone, as the prophet, can defeat Lavos. He knows from his time as a child that if Chrono is there that the event is all but guaranteed to play out the same way it did before. Magus believes the entire time that he is saving Zeal and his sister Schala but what he does not realize is that the actions he takes as the prophet were unchanged and by locking out Chrono it leads him and the gang to 2300 AD where they obtain the wings of time.
Magus is trying to save Zeal. He wages the war in 600 AD as a way to summon Lavos in the hopes his time traveling abilities send Magus back to 10000BC where he can save Schala. When Lavos finally does awaken it just so happens to be when Magus is fighting Chrono and Frog. Magus would likely believe at that point that first and foremost in order for history not to repeat that Chrono and his gang must be banished because A) they have not seen what he's seen and thus have no idea how to help him and B) he knows them being there increases the liklihood of everything happening the same way again which is precisely what he's trying to avoid.
Because Magus is so focused on saving his Sister he is never able to understand that the actions he takes as the prophet, trying to save Zeal, are actually what causes Zeal and his Sister to die. It is only after the 10000BC world is flooded/destroyed by the collapse of the sky civilization that Magus, standing at the North Cape, finally realizes the actions he took trying to save Zeal are in fact what cause Zeal and his Sister to be destroyed.
Magus is truly the most tragic figure in the entire game because of this...
This is also why, imo, shortly after Chrono's death when Frog and the Gang find Magus on the North Cape - watching the world sink before him as he comes to the aforementioned tragic revelation - Magus wants the Frog to finally fight him, and kill him, because he cannot live knowing that his entire life's work of summoning Lavos to save his sister is actually what causes his sister to die.
Consider the conversation he has then with the Frog...
Magus: Unimaginable is the power of Lavos. Anyone who dares to oppose it... meets certain doom. At this rate, you too, will meet a hideous fate. Just like that poor fool, Crono!
Frog: You dare to insult him?
Magus: He's history! Play with fire and you get burned.
Is he actually talking about Crono or himself?
You as the player have the choice to put him out of his misery in that moment or allow him to redeem himself by letting you know how to bring Chrono back from the dead (knowledge I imagine he had by researching it for Schala's sake.) and allowing him to join you in your fight to finally kill Lavos once and for all.
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