(Going ahead a couple days and cutting to Team Rocket...)
A day or two later, in an undisclosed location...
With a strained groan, Mewtwo cracked open an eye, finding himself on the floor of a dimly-lit room. His head felt as if it weighed fifty pounds, and he swam through a gelatinous sea of pain, fatigue, and mental fog. The tight band around his chest had gone, as he could breathe easier. His mouth tasted like metal and dirt, and a thick, sticky film coated his tongue and throat. He groaned again, opened his eyes, and lifted his head. "...Where am I...?"
Lights above him snapped on, assaulting his sensitive vision. Mewtwo winced and turned his head from the optical onslaught. The light sent a stab of pain through the front of his head, and turning it only served to intensify the feeling. He reeled and finally managed to haul himself up onto his elbows.
"Took you long enough to wake up," a voice from the opposite end of the room announced. Mewtwo slowly and carefully turned his head--it felt as if it were a dead weight balanced precariously on his shoulders--seeing that blonde woman, Domino, standing there, separated from him by what he assumed was glass. Domino conversed briefly through an intercom before turning her gaze to him, smirking. "Those drugs really knocked you for a loop."
Mewtwo did not respond to her comment. His eyelids felt heavy and that mental fog had not cleared, though he could at the very least tell that it was not caused by that altered Alakazam. This feeling was most certainly drug-related.
"By the way," Domino fixed him in her glare, "that extra dose of muscle relaxers was from me. Payment for Mt. Quena."
Mewtwo's ears perked up. "How did you know...?" He had wiped her memory! There was no way she could have remembered that!
Domino's glare darkened. "I have a great hypnotherapist, specializes in repressed memories. And, it wasn't cheap. I had to write it off as treatment for another mission! Do you know what it cost me?" She stepped forward. "My record now claims that I have PTSD! I almost lost my job because of you!" She put her hand on the glass before her as her voice deepened into a vicious warning. "So help you if Giovanni ever remembers..."
Mewtwo didn't need to think about the consequences. Domino's warning was enough.
Domino stepped back. "That's water under the bridge, Mewtwo. And we'll keep it between us. Should you choose to defy me, though, I have absolutely no problem with telling my boss about your betrayal. I'm sure he'll be thrilled to hear how you wiped his memory." Her tone carried an edge of venom. "In the meantime, you should get comfortable. You're going to be with us for a long time." Chuckling, she turned and walked away.
Mewtwo watched her leave. He took a moment to look about the room. It had a strange smell, the likes of which he could not identify. The floor beneath him felt tacky, and he could reasonably assume that the observation window was not constructed simply of glass. They were fully aware of his destructive capabilities and would not be so stupid as to merely stuff him into a simple cell. There was more to this room than he realized, and the smell had something to do with it.
With another groan, Mewtwo managed to pull himself on all fours, and then finally to a crouch, all the while taking care not to move his head so much, or as suddenly. Idly, he wondered where Dr. Wily was...