A possible plot could be that there is a powerful and mysterious force that is causing chaos in different parts of the world. Both Lara Croft and Wonder Woman are independently investigating it. Eventually, they meet and decide to team up. They travel to different locations, from ancient ruins to modern cities. During their journey, they exchange stories about their past adventures and develop a mutual respect. They then use their combined knowledge and powers to track down the source of the chaos, which turns out to be a mad scientist who wants to use the power of the gods for his own gain.
Well, perhaps in the fanfiction, Lara Croft is exploring an uncharted planet when she stumbles upon a Halo ring. This attracts the attention of the Covenant, and Master Chief arrives to deal with the situation. At first, there's some tension between them as they come from different worlds and ways of doing things. But as they start to understand each other's motives and skills, they combine Lara's knowledge of ancient mysteries and Master Chief's combat expertise to fight the Covenant and figure out the secrets of the Halo ring.
Athanatos could be a great villain. He's a powerful and immortal being who has been sealed away for centuries. But with the disruption of ancient magic (maybe caused by Lara's latest adventure), he is freed. He wants to conquer both the mortal and the Amazonian worlds. Lara's knowledge of archaeology and Wonder Woman's combat skills would be put to the test against his dark magic.
One idea could be that Lara Croft is exploring an ancient tomb and stumbles upon a hidden Umbrella Corporation facility. She discovers that they were experimenting with some sort of ancient virus that was sealed in the tomb long ago. The T - virus has escaped and is starting to mutate the local wildlife and some of the tomb's guardians. Lara has to team up with a Resident Evil character, like Jill Valentine, to stop the virus from spreading further and also figure out how to deal with the newly awakened threats in the tomb.
One possible plot could be Lara Croft discovers a Prothean artifact during one of her adventures. This artifact has a connection to the Mass Effect universe, perhaps it contains data about the Reapers. She teams up with Commander Shepard to figure out how to use this information to stop the Reapers or some other threat that is starting to cross over from the Mass Effect universe into her world.
Well, one possibility could be that Naruto, with his ninja skills, teams up with Lara Croft in a tomb raiding adventure. Maybe they are searching for a powerful artifact that has ties to both their worlds. Naruto could use his shadow clones to help in exploring different areas of the tomb at the same time, while Lara uses her knowledge of ancient languages and traps.
Maybe there's a powerful ancient artifact that has been stolen and is being used for evil purposes. This artifact has the power to disrupt the balance between different realms. Spiderman discovers some strange happenings in the city related to the artifact's power, like buildings randomly changing shape. Wonder Woman is also on the hunt for the artifact as it was stolen from a place under her protection. When they meet, Spiderman is initially in awe of Wonder Woman's strength and beauty. They team up, with Spiderman using his acrobatic skills to navigate through dangerous traps set up by the villains protecting the artifact, and Wonder Woman using her lasso of truth to find out where the artifact is hidden.
One possible plot could be that Naruto is somehow transported to the DC universe. He meets Wonder Woman and they have to team up to stop an enemy that is using a combination of chakra - based jutsu and advanced technology from both their worlds. Naruto's ability to sense and manipulate chakra could be a great asset in the DC universe filled with various super - powers.
A Tomb Raider and Uncharted crossover fanfiction could be about Lara Croft and Nathan Drake teaming up. Maybe they start off as rivals, both after the same ancient artifact. But as they face various traps and enemies, they realize they need to work together. They could share their skills, with Lara's survival skills and Nathan's sense of adventure complementing each other.
A crossover with the Assassin's Creed series could also work well. Lara Croft might find herself in the middle of the conflict between the Assassins and the Templars. She could learn about their hidden history and use their ancient techniques while still relying on her own methods of survival and discovery.
One possible plot could be that a powerful new villain emerges that threatens both the Marvel Universe and Wonder Woman's world. The Avengers and Wonder Woman cross paths while investigating the strange occurrences related to this villain. They initially have some clashes due to their different methods and cultures, but then realize they need to work together. For example, Iron Man might be impressed with Wonder Woman's indestructible bracelets and try to analyze them, while Wonder Woman could learn about modern technology from Stark. Eventually, they combine their powers and skills to defeat the villain.