Here's the Cliff Notes version, Phi:
Mewtwo caused a ruckus. He's in trouble.
Carr caused a ruckus disguised as Mewtwo. He's in trouble, and Mewtwo is in double trouble for that, because of Bitchy Jenny.
Team Rocket might be causing a ruckus, but we're not sure, but they want Mewtwo back, so they're going to try the legal approach.
Team Rocket and Cipher are hooking up, but they've kept Domino in the dark about it, and she's pissed because she thinks the team-up is trouble, but that's not anything that Phoenix needs to worry about. However, the Team Rocket presence in the Pokemon Institute is cause for concern.
Quickie and Wily need a good lawyer to help them win the case and keep the state from handing Mewtwo over to Team Rocket, or deporting his purple fuzzy butt if both sides lose.