Perhaps they time travel to a parallel universe. In this universe, Darth Vader never turned to the dark side and Anakin Skywalker remained a Jedi. Luke would be able to see how different things could have been. This experience might inspire Vader in their own universe to try and find a way back to the light side, and they could then work together to bring positive change to their own timeline.
One idea could be a story where Darth Vader secretly trains Luke in the ways of the Force before Luke fully realizes who he is. This would add an interesting layer of secrecy and moral conflict for Vader.
One idea could be a story where Luke discovers a way to temporarily reverse Vader's Sith corruption, leading to some heart - to - heart conversations between them as Anakin. Another could be a fanfic where they have to team up against a new, greater threat in the galaxy that neither the Rebels nor the Empire can handle alone. Maybe a story where Luke gets trapped in a Sith - created alternate dimension and Vader has to go in and rescue him to atone for his sins.
A great plot idea could be that Darth Vader is ordered by the Emperor to kill Baby Luke, but he can't bring himself to do it. Instead, he fakes the baby's death and takes him to a hidden Jedi enclave. There, with the help of some remaining Jedi, they start to train Luke in secret. Meanwhile, Vader has to constantly deceive the Emperor about Luke's whereabouts and his own actions regarding the boy. This would create a lot of tension and drama in the fanfiction as Vader is walking a very dangerous line between the dark side and a newfound sense of hope through the baby.
One interesting plot could be Darth Vader traveling back in time to prevent his own fall to the dark side. He might try to change the events that led him to become Vader, like saving Padmé. Another could be Vader traveling to the future and seeing the downfall of the Sith, which makes him question his loyalty to the dark side. He could then try to find a way to change the future of the Sith order.
One idea could be exploring Darth Vader's identity before he became encased in the suit. Maybe he rediscovers his old self and tries to reconnect with his past relationships. Another could be him having to face the Jedi without the intimidating suit, relying solely on his raw Force abilities.
Perhaps Darth Vader's dark side powers are misinterpreted in the Naruto world as a new and extremely dangerous form of jutsu. Naruto and his friends might try to find a way to seal these powers. Meanwhile, Vader is on a quest to find a way back to his own universe, and in the process, he starts to question his own dark ways after seeing the camaraderie among the Naruto characters. He could end up having a change of heart and use his powers for good in the Naruto universe.
One idea could be a story where Darth Vader discovers Leia's true identity earlier and struggles with his loyalty to the Empire and his newfound knowledge of his daughter. He could secretly protect her from the Emperor's wrath.
Another plotline could involve them traveling to the future. Maybe they see a world where the Jedi have been fully restored and are working in harmony with the galaxy. This could make Vader question his past actions even more, and Luke could gain new insights into the future of the Jedi Order.
Their relationship could become more understanding. As they travel through time and see different events together, Luke would gain a deeper understanding of what led his father to become Darth Vader. Vader, in turn, might see Luke's unwavering hope and goodness more clearly, which could soften his stance.
Another plot could be set in an alternate universe where Ahsoka manages to reach out to the little bit of Anakin still left in Darth Vader. She tries to redeem him, and through a series of encounters, they start to question their own paths and the Sith vs. Jedi ideology.