The story would be very different. The loyalty of the other characters would be tested. For example, Annabeth might be heartbroken and try to bring Percy back to the right side. Also, the gods would be in a much more difficult situation as they face a combined threat of Percy and Kronos.
In a fanfic scenario where Percy Jackson joins Kronos, it could be a very interesting exploration of the 'what - ifs'. Percy has a strong sense of justice, so for him to side with Kronos, Kronos must have presented a very convincing argument. It could be that Kronos showed Percy a future where the demigods are constantly oppressed by the Olympians. However, this would also mean Percy has to go against his instincts and the relationships he has built. His friends like Annabeth would be in shock and try to bring him back to the right side. This could lead to some intense battles not only between the demigods and Kronos' forces but also within Percy himself as he struggles with his new allegiance.
If Percy Jackson joins Kronos in fanfiction, it would be a huge deviation from the original story. Percy is a hero who stands for good, and Kronos is a villain. This could lead to a very dark and twisted version of the Percy Jackson universe, with Percy using his powers to aid Kronos in his evil plans, perhaps causing chaos among the gods and other demigods.
Well, in this fanfiction, Percy might face a huge moral dilemma. Since Kronos is a villain, Percy joining him could be a really dark turn. Maybe he's been tricked or is trying to stop Kronos from the inside. It could lead to some intense battles within the Titan's ranks as Percy tries to figure out his true loyalties.
One way for Kronos to win in Percy Jackson fanfiction is by spreading more chaos and discord. If he could make the demigods lose faith in the gods and each other, his job would be much easier. He could also try to find a way to use the prophecies to his advantage. Maybe he could twist the words of the prophecies to make the demigods make wrong decisions. And if he could somehow break the connection between the demigods and their godly parents, the demigods would be weaker and he could overpower them.
The story could progress with Percy becoming a sort of anti - hero. He might start by using his powers to disrupt the balance that the gods have maintained. Gaea could use him to target the other demigods first. For example, he could lead attacks on Camp Half - Blood.
In fanfiction, Kronos's role is not just limited to being a villain. Sometimes, he can be a catalyst for character development among the demigods. His actions force the heroes to become stronger, both physically and mentally. For instance, his threat might make Percy Jackson more determined to master his powers. Also, Kronos can be used to introduce new plot elements, like a new weapon or a magical item that has the power to stop him.
One great Kronos fanfiction could be about his backstory before he turned evil. Maybe it explores his relationship with the other Titans and what led him to start the war against the Olympians.
Percy's reaction could also be one of self - doubt. He may start to question his own actions and leadership. He might think that he has done something wrong to push Annabeth away. However, his loyalty to his friends and the cause would eventually make him stand up against Kronos and try to bring Annabeth back to the right side.
The other Titans could be main antagonists. For example, Hyperion who is known for his great strength and his desire for destruction. He might not fully trust Percy and constantly try to undermine him in Kronos' eyes. Another could be Atlas, who is already a major foe in the Percy Jackson series. He might see Percy as a threat to his own plans within Kronos' regime.
Well, one possible plot could be Percy having to hide his relation to Kronos while still fighting against the Titans. He might struggle with the internal conflict of having a connection to such an evil entity as Kronos while trying to protect his friends at Camp Half - Blood.