Perhaps Percy finds out that the Trojan War was actually started by a powerful, ancient evil that the gods are using the war to cover up. He then has to decide whether to continue fighting for the Greeks or try to expose the real cause of the war, which would put him at odds with both the Greeks and the Trojans.
Well, one plot twist could be that Percy discovers he has a hidden connection to one of the major Trojan heroes. Maybe he finds out he's related to Hector in some way, which makes his fight against the Trojans much more complicated. He might struggle with his loyalty to the Greeks.
One possible plot twist could be Percy finding out that a fellow soldier is actually a spy from the enemy side. This would create a lot of internal conflict as he has to decide what to do about it.
Some of the Greek heroes like Achilles could be Percy's allies. Percy might learn a lot from Achilles about combat and heroism. And there could be some new characters created specifically for this fanfiction, like a young seer who can predict the outcome of battles and helps Percy make the right decisions.
A really interesting plot twist might be that Voldemort and Percy are forced to team up against a common enemy. They realize that there is a greater threat that neither of them can face alone. This would be a huge change in their relationship as they are initially enemies. Or perhaps Percy discovers that he has some latent wizarding abilities due to his godly heritage, which completely changes the dynamics of the fight as he can now use both his demigod powers and magic.
A great plot twist could be that Naruto is actually a demigod in the Percy Jackson sense all along. Maybe his parents were from the world of Greek gods but were sent to the Naruto universe for some reason. Another twist could be that the God of War, say Kratos, is actually related to one of the main clans in the Naruto world. This would completely change the power dynamics and relationships in the fanfiction.
One possible plot twist could be that Sakura discovers a hidden weakness of Madara's during the fight. Maybe it's a chakra point that, when struck, temporarily paralyzes him, giving her an upper hand.
Well, a possible plot twist is that their powers combine during the fight. Like, Percy's water and Jason's lightning create some sort of new, powerful energy that neither of them can control at first. This could lead to them having to work together to contain it. Another plot twist could be that the fight is a dream or a vision, and they both wake up in different places realizing that they need to prevent this fight from happening in the real world. And perhaps there's a prophecy that says one of them must die in this fight, but they find a way to change the prophecy during the battle.
Well, it could be that Percy is fighting Ares to protect his friends. Maybe Ares has threatened Percy's loved ones in Camp Half - Blood, so Percy has no choice but to face the god of war.
Well, it ended because of the clever ruse of the Trojan Horse. The Greeks pretended to sail away, leaving the horse as an offering. The Trojans were deceived and took it in. Once inside the city walls, the hidden Greek soldiers launched a surprise attack. This led to the downfall of Troy and the end of the war. The Greeks were able to defeat the Trojans after this strategic move.
Fiction. The idea of the Trojan Horse is a great story but there's no evidence to suggest such a large wooden horse was used in a real war. It was probably a creative addition to the legend to make the story more exciting.
Maybe there is a scientist or an inventor who becomes Percy's ally. This person could be creating new weapons or gadgets that Percy uses in battle. Their alliance could be crucial in giving Percy an edge in the fight. For example, the inventor might create a special type of grenade or a device that can jam the enemy's communication lines.