A plot twist could be that they are joined by other Jedi who also believe that the Dark Side has been misjudged. Together, they form a new order that tries to balance the Light and Dark. But this new order is seen as a threat by both the Jedi and the Sith. So Anakin and Obi - Wan have to fight on two fronts, against those who once were their allies and against the true Sith Lords who want to use them for their own evil purposes.
Maybe the Force itself could be an antagonist in a sense. The light side of the Force would be trying to pull Obi - Wan back from the dark side. And the natural balance of the Force that doesn't want too much dark side influence could be working against Anakin's plan to turn Obi - Wan. So the Force, in its own way, could be the main antagonist.
Perhaps Anakin manipulates Obi - Wan's emotions towards him. Anakin could play on their brotherly bond and twist it. He might make Obi - Wan think that by joining the dark side, they can save more lives together. Anakin could also introduce Obi - Wan to some dark side teachings that seem appealing at first glance.
A possible plot twist could be that Obi - Wan was actually faking being turned to the dark side all along. He was trying to infiltrate the Sith ranks to learn their secrets and stop them from within. He lets Anakin think he has succeeded in turning him, but in reality, he is still a Jedi at heart and has a plan to take down the Sith.
One way could be to explore the idea of a great betrayal. Maybe a powerful Sith Lord manipulates events in such a way that Anakin and Obi - Wan both feel they have no other choice but to side with the Dark Side. For Anakin, it could be something related to his fear of losing Padmé, and for Obi - Wan, perhaps the Jedi Order's actions against him make him lose faith. The story could start with a series of small incidents that gradually push them towards the Dark Side.
Maybe Anakin uses a Sith artifact that has the power to influence minds. He manages to expose Obi - Wan to it without his knowledge. The artifact starts to corrupt Obi - Wan's thoughts, making him more aggressive and less Jedi - like. Anakin then further fuels this change by constantly challenging Obi - Wan's beliefs and actions, slowly pushing him towards the dark side.
In this kind of fanfiction scenario, it would be a huge shock to the Star Wars universe. Obi - Wan is known for his strong connection to the light side. If he turned, perhaps his relationship with Anakin would have been drastically different. Instead of being a mentor, he might have been a rival or even a corrupting influence on Anakin.
Well, if Obi Wan turned to the dark side in fanfiction, it would likely shake up the dynamics between him and the other Jedi. It might also change the outcome of many key battles and events in the Star Wars universe.
Count Dooku could be a prominent character. Given his own fall to the dark side, he might be a mentor or a rival to Obi - Wan in the fanfiction. Mace Windu is another one. His strict view of the Jedi Code and his relationship with Obi - Wan could be explored in the context of Obi - Wan's turn. And of course, there are the various Sith Lords and dark side adepts that might surround Obi - Wan, either as allies or enemies in his new dark side life.
One common theme is the struggle between light and dark within Obi - Wan. It shows how he might battle his own inner demons. Another is the impact on his relationships, like with Anakin or the Jedi Order.