Even though it is a legendary, Mewtwo hooked to a PULSE machine could be bad. Think of the power-hungry pokemon Mewtwo is, with the ability to stay in his pulse and levitate the PULSE to move himself. IT COULD CAUSE WORLD DEVASTATION.
On a more serious note:
Step 1: Hook up a Pokemon with Earthquake to the PULSE machine, and amplify the quakes to shake the city to the ground.
Step 2: Hook up a Porygon with Recycle to the PULSE, and make him recycle the rubble ( and dead people ) back into the enviroment, clearing the land and restoring the natural area of reborn.
Step 3: Hook up an owned Alakazam (so it will listen, unlike abra) to the pulse machine, and use his psychic powers to detect all the survivors, and teleport them to us, where they can be easily outnumbered and dealt with.
Step 4: Dig back down to the door, (you would have found the 4 keys once you grabbed all the survivors, or when porygon was recycling) and open the door to obtain the power inside.
Step 5: Use power to build a new civilization, where the most worthy and honorable rules, with the people having the ability to overthrow and re-elect a new ruler.
Step 6: Rule.
Step 7: Pokemon start to return to the land, the natural enviroment having been restored.
Step 8: Set up a fundamental system of only allowing people to have certain pokemon, thus preventing anybody from becoming strong enough to challenge your rule.
Step 9: Basically a series of events happens to rebuild "Reborn" under a different name. You hide the power in a greedy attempt to stop anyone else from ruling. A new team "x" arises to challenge your power, and you seal it away, splitting the gemstone key into 4 pieces and scattering the remnants. Random villagers find them and pass them down in their family, and the process indefinitely repeats.
Step 10: THERE IS NO STEP 10.