Maybe a character from Glee could gain superpowers like the ones in Flash. For example, a Glee character could accidentally get exposed to some meta - human - creating substance and then have to learn to control their new powers with the help of the Flash team.
A crossover could involve the Flash running into the Glee club while they are on a trip. He could be intrigued by their music and energy, and they could end up collaborating on a project to raise awareness about something important in both their worlds.
One idea could be to have the characters from Glee perform at a Central City event in the Flash universe. They could sing a song to boost the morale of the citizens during a time of crisis.
One plot idea could be that a character from Flash, like Barry Allen, somehow gets zapped into the Glee universe. He could be confused by all the singing and dancing at first, but then use his speed to help the Glee club prepare for a big competition in a very short time. For example, he could quickly gather all the necessary props or help the members with their choreography by demonstrating moves at super - speed.
One idea could be that the characters from Glee find themselves in Central City during one of The Flash's battles. Maybe they get caught in the crossfire and The Flash has to save them while also dealing with the meta - human threat. For example, Rachel could be singing on the street when a meta - human causes chaos nearby.
Another concept is that a villain from The Flash's world uses the power of music (inspired by the Glee club's performances) to create chaos. The Flash teams up with the Glee club to reverse the effects of the music - based villainy. The Glee kids could use their knowledge of harmony and rhythm to counter the negative musical energy, while the Flash uses his speed to stop the physical manifestations of the villain's attacks.
One idea could be Hermione using her magic to enhance the Glee Club's performances. For example, she could create amazing stage effects with spells. Another could be her helping the members of Glee with their studies, like tutoring them in difficult subjects. Maybe she could also introduce some wizarding world music to the Glee Club which has a completely different style and rhythm.
Another possible storyline is that a villain from the Flash's world somehow ends up in the Glee universe and starts causing trouble. The Glee club members, with the help of the Flash (or someone with Flash - like powers), have to come together to defeat the villain. They could use their unique skills, like singing in harmony to disrupt the villain's powers or something equally creative.
One idea could be that a supernatural entity from the Supernatural world somehow ends up in Central City and starts causing chaos that only the Flash's speed can help contain. For example, a demon that can possess multiple people at once and the Flash has to use his speed to track down all the possessed bodies before the demon can complete a dark ritual.
One idea could be that Flash and Supergirl team up to stop a powerful alien villain who is causing chaos across both their cities. The villain could have the ability to manipulate time and space, which would make it a real challenge for the two heroes.
One idea could be that the Glee club is invited to perform at a big event in National City where Supergirl is also present. They could end up teaming up to save the day when an alien threat targets the event. The Glee kids' unique talents could be used in unexpected ways, like using their voices to disrupt an alien's sonic weapon.
A Reverse Flash crossover with the Flashpoint timeline could also be great. The Reverse Flash could try to further manipulate the already - altered Flashpoint world. This could involve him trying to turn heroes into villains and vice versa, causing chaos in a world that is already on the brink of collapse.
A cool concept for twilight and flash crossover fanfiction could be a time - travel aspect. What if a character from The Flash travels back in time and accidentally alters the history of the Twilight world? This could lead to all sorts of chaos, like vampires ruling the world instead of just being in hiding. Or, a Twilight character could use the Flash's speed - related technology to gain an edge in their own battles, like using it to quickly escape from a werewolf pack.