Perhaps the main antagonist could be Loki himself, at least in the beginning. Since he got involved with Thanos' legs in some improper way, Thanos might see him as the antagonist. But as the story progresses, they might find a common enemy. So, initially, Loki's actions and motives that revolve around the legs could make him the antagonist in Thanos' eyes.
Well, perhaps in this fanfiction, Loki is cursed to be attached to Thanos' legs for a period of time. This forces them to work together in a very strange way. Loki tries to use his wits to find a way to break the curse, while Thanos is frustrated by Loki's constant attempts at trickery. Along the way, they might encounter other characters from the Marvel universe who are both amused and confused by their situation.
Well, it could be something like Thanos becomes intrigued by Loki's legs for some strange, otherworldly reason. Maybe Loki has some sort of magic or power that is centered around his legs that Thanos wants to possess or control.
You might try fanfiction websites like Archive of Our Own (AO3). They have a large collection of fan - created works. Just use the search function and type in 'Thanos x Loki' and see if there are any stories related to the specific 'legs' aspect you're interested in.
It could be Thanos. Since he is a powerful and menacing force in Loki's universe. He might see Harry as an unexpected variable and want to eliminate him. Also, his goal of collecting the Infinity Stones could put him at odds with both Harry and Loki as they might try to stop him to protect their respective worlds.
It could be someone who is manipulating Loki to kidnap the Hulk. Maybe an even more powerful villain from the Marvel universe, like Thanos. He might be using Loki as a pawn to get the Hulk for his own evil purposes.
Loki and Thanos are the central figures. However, characters from Loki's family such as Thor could also be significant. Thor might notice the changes in Loki and try to rescue him from Thanos' control. Additionally, characters like Heimdall, who has the ability to see across the realms, could be involved in detecting Loki's unusual behavior and Thanos' influence.
I'm not sure specifically about Loki x Thanos mpreg fanfiction. Fanfiction can cover a vast range of pairings and themes, but this particular one might be quite rare or not very mainstream. You could try searching on some large fanfiction platforms like Archive of Our Own to see if there are any works of this kind.
Power is a common theme. Both Thanos and Loki are power - hungry in their own ways. In fanfictions, they often either compete for power or try to use each other's power for their own goals. Another theme is redemption. Sometimes Loki is seen as a way for Thanos to find redemption, or vice versa.
In a different take, a new character could be introduced as the main antagonist. Maybe a criminal mastermind who teams up with the Joker specifically to target Robin. This new character could have a personal vendetta against Robin or see him as a key to achieving some greater evil plan, and the Joker is just a means to an end in this scenario.
It could be Kaguya Otsutsuki. Since she has powerful abilities and a thirst for power, she would see Kefla's power as a threat and Naruto's influence as something to be eliminated. She might try to manipulate events to turn the ninja world against Kefla and Naruto.