One idea could be a story where Ace teams up with Supergirl against the Joker's evil schemes in the Young Justice universe. Maybe Ace has some special abilities that complement Supergirl's powers.
Perhaps in the fanfiction, the Joker has created a mind - control device and is using it on some of the Young Justice members. Supergirl and Ace must figure out how to stop him and free their friends. Supergirl could use her strength and flight abilities while Ace uses his wits and any special skills he has.
A more complex plot could involve Ace having a hidden connection to the Joker that is slowly revealed. For example, Ace could be an experiment of the Joker's from the past that has now joined Young Justice, and the story could explore how this connection affects both Ace and the team.
You can try fanfiction platforms like Archive of Our Own (AO3). It has a large collection of Young Justice fanfictions that might feature Ace and Joker. Just use the search function and type in relevant keywords.
One idea could be exploring the clone's struggle with identity. Is it doomed to be evil like the Joker or can it break free? Maybe it starts to have glimmers of goodness when it interacts with the Young Justice team.
One great fanfiction idea could be that Superboy discovers Lois Lane's hidden powers. Maybe in this Young Justice universe, Lois has some latent psychic abilities that only Superboy can sense. He then has to protect her from a new villain who wants to use her powers for evil.
One plot idea could be that Supergirl, while on a mission in a new city, accidentally crosses paths with the Young Justice team. They initially mistake her for an enemy due to her Kryptonian powers being so strong. But as they get to know her, they realize she can be a great ally. Another idea is that there's a powerful villain who is specifically targeting Kryptonians and the Young Justice team has to work with Supergirl to stop this threat. They might learn new fighting techniques from each other during the process.
One great 'Young Justice Joker Fanfiction' is 'Joker's Gambit'. It shows an interesting take on how the Joker might interact with the Young Justice team. The story is full of suspense and the characterizations are really well - done.
In many Young Justice fanfictions, Supergirl can be portrayed in various ways. Sometimes she's shown as a powerful and somewhat naive newcomer to the team. She might struggle to fit in with Earth's customs while still being eager to prove herself. For example, she could be depicted as being overly enthusiastic in battles, which might cause some initial friction with the more experienced members of the team.
One idea could be to create an OC who is a former victim of the Joker's madness and now has powers as a result. They could join the Young Justice team to seek revenge against the Joker. Another idea is an OC who is related to an existing character in the Young Justice universe and is lured into the Joker's chaotic world. For example, a relative of Robin who the Joker tries to corrupt.
There's a fanfic called 'Nightwing and Supergirl: United Front' which has great character interactions. It shows how they work together in battle and also their off - battle banter which is really engaging.