Maybe a villain from the dimension where Wally has been. This villain could have followed Wally back to seek revenge or to take over the world that Wally has come back to. Since Wally has some knowledge about this villain, it would be his responsibility to stop the villain and protect his friends and the world. The villain might have powers that are a match for Wally's, making it a really tough fight.
It could be a new villain who has a vendetta against speedsters. Since Wally is a speedster, this villain might see his return as an opportunity to prove himself. Maybe he's a scientist who has developed a weapon specifically designed to counter speedsters' abilities.
Maybe Wally returns with new superpowers. He could surprise his old friends in Young Justice and they all go on a new mission together.
The Reach could be a great antagonist. They might see Kid Flash's return as a threat to their plans for Earth. They could try to capture him and study his powers to find a way to counter the other heroes. Since they are an alien race with advanced technology and devious plans, they would pose a significant challenge for the 'Young Justice' team.
In a 'Young Justice Outsiders Wally Returns' fanfiction, he might return as a changed person. He could have lost his memories while away and slowly regain them as he interacts with his old friends. His return could also bring back old threats that were thought to be gone. For example, an enemy from his past might resurface, believing that Wally holds the key to something they want.
Well, it could be that Wally returns with new superpowers. Maybe he was in some sort of time - warp or alternate dimension and comes back stronger. He might have to prove himself to the team again that he's still the same Wally they knew.
Wally could be developed by showing his growth in character. For example, if he was a bit cocky before, he could return more humble and with a deeper understanding of the world. This change could be a result of his experiences while he was away.
The League of Shadows could be a great antagonist. They might see Young Justice as a threat to their plans in the world and Batgirl as an obstacle in Gotham. They could try to manipulate situations to make Young Justice and Batgirl turn against each other while they carry out their own devious plans, like releasing a dangerous virus in a major city.
It could be a powerful sorcerer. This sorcerer might be trying to capture the Ghost Girl's essence for his own dark magic. He sees her as a source of great power because of her unique ghostly nature.
A new, original character could be created as the antagonist. Maybe a powerful and vengeful assassin who has a grudge against Robin for some past event. This character could have unique abilities and a personal vendetta that drives the conflict in the fanfiction.
The Joker could be a great antagonist. He might have captured Robin for his own twisted games and is holding him hostage in some elaborate death - trap. The Young Justice team would then have to outwit the Joker to get Robin back.