Rei is basically trying to eradicate all pokemon by making a wish on Jirachi, and he leads Team Enel, of course. That much can be seen as obvious, since that's most of my plots. However, while you're going on your gym quest, it gets cut off after the 4th badge, so you can't fight any more gyms.
Those are a couple of details, now I can get onto the whole story arc of the two-part hack. (There will be two games in this)
Pokemon Black Crystal: Enel: Rei invades and forms Team Enel, who are stealing from people and killing pokemon to obtain resources so they could find Jirachi, however, they are rivalled by the criminals who want to be free to do what they want, which happens to be the same thing, sans the exterminating pokemon part. Eventually, you side with the criminals, and take down Team Enel.
After the storyline, where the region is beginning to go down the drain, there are two people, Marcus and Drake, who are taking advantage of this by running for office. Normally this wouldn't be a bad thing, but you notice a small symbol of Enel wherever they appear that no one else sees, since it was never shown to them. So you chase them to a volcano, and fight them.
Pokemon Black Crystal: Licentia: After 30 years, the region is now a third-world region now. Its pokemon league is a thing of the past, and half of the country is ruled by criminals, who named their group Licentia. After the events of Platinum, Cyrus runs into the region, and is offered a choice to join them. He refuses, wanting time to think of his own plans, but he gets chased out. The police catch him, and force him to take care of the threat with new pokemon.
He goes around combating Licentia wherever they pop up. The first game, I don't care if it's spoiled a bit, but the second game's plot I want to keep in my head for now. But trust me, it will be great. And yes, you play as Cyrus... the same one from Platinum.
That's the plot in a nutshell, I guess.