Meanwhile, in Viridian City...
Giovanni walked down the dark corridor in the basement of his gym complex. A few of the Pokemon in the cages flanking the hallway let out their cries, and others just watched him in silence. Giovanni smirked slightly as he walked. He could hear the howls of protest from that fanatical Pokemon protection group now. Thankfully, their college campus ilk had not staged a protest on his grounds for a while. His lawyers had made sure of that.
Turning a corner, he walked down a long hallway, passed several doors, and to a locked door at the end. Inputting his passcode and swiping his card, he unlocked and opened the door, stepping through and allowing it to close and secure behind him. He descended a flight of stairs, accessed another locked door with a different set of codes and cards, and emerged in a large, sterile corridor. The area was well-lighted, the walls white. His shoes clicked across the polished floor as he approached yet another locked door, accessed it with yet another sequence of codes, cards, and keys, and stepped into the anteroom. He was immediately greeted by one of his assistants, who presented him with a set of disposable coveralls, which Giovanni quickly donned. He secured the hood around his head, put on the goggles and mask given to him, slipped his hands into a pair of gloves, and followed the assistant in silence through what amounted to an airlock, where he and the assistant were doused in a disinfectant spray. Finally emerging from the airlock and into the laboratory, Giovanni finally spoke.
"So, have you found anything?"
The assistant nodded quickly and handed him off to Domino, who was similarly dressed in white coveralls. Domino gave a nod as she addressed Giovanni. "Though, you didn't request it, we had AC-065-Σ trace the sample of litter. It managed to get a lock on our target. With your permission, we'd like to proceed with the operation."
Giovanni gave a nod. He knew that the augmented Alakazam was powerful, but he was not fully aware of the extent of its abilities. Unfortunately, due to the nature of the experiment, the creature could not be kept in the gym, nor be used for battle. Giovanni's scientists had implanted circuits into the Alakazam's brain, and it was permanently connected to the computer. Due to the exposed circuitry and brain tissue, the area needed to be kept sterile, hence the urgency of having Giovanni dress in what he equated to being a garbage bag.
Giovanni walked through the lab, to the chamber where AC-065-Σ was kept. The enhancements had provided Giovanni with a powerful tool, though it had robbed the Alakazam of any semblance of life. The Pokemon gazed at him with blank eyes, wires snaking from a metal halo that had been fitted into the creature's opened skull. The Alakazam was a puppet. A powerful puppet, but a puppet nonetheless. However, for his own purposes, a puppet was all that Giovanni needed.
"You may proceed as planned," Giovanni gave a nod of assent. Out of the corner of his eye, he could see Domino command another technician, who turned their attention back to their computer screen. The Alakazam could no longer perceive verbal commands, and all of its information was fed straight to its brain. It was far more effective that way.
Giovanni sneered behind his mask as he stepped back from the chamber. For the first time that he had witnessed, a spark of life could be seen in the Alakazam's eyes. It had received its orders. It knew what it had to do.