The Keystones are three magical amplifiers of solid elemental ectoplasm. They appear in the 2003 TV series episode Past and Present.
As the Shredder Tengu and his Foot Mystics begin to transform New York City, Splinter and the Ancient One tell the Turtles, April O'Neil, Casey Jones, Karai and Dr. Chaplin about ley lines. Ley lines, they explain, are hidden conduits of mystic energy that run throughout the planet and an uncommon number of those lines converge in New York - in three specific places.
The Ancient One indicates the three areas of convergence on a map on April's computer. Karai then mentions "Keystones" and looks to Chaplin. He says that when the Mystics escaped Karai's control, the two of them did a lot of research into their magic and what they'd been up to on the sly. They learned that for decades, the Shredder’s mystics blackmailed city officials into installing three Keystones around the city. One at the Statue of Liberty, one at the United Nations building, and one at Manny’s Meats in Northern Manhattan. Chaplin says that seeing as the Keystones are set on junctions of ley lines, whoever controls them would have control over the mystic energies of the whole planet.
The group decides that if they have access the Keystones before Shredder and focus their energy into them, that perhaps they could reverse the demon's spell and cripple Shredder in the process.
To this end, three teams are dispatched to the Keystones: Leonardo, Karai and the Ancient One go to the Statue of Liberty, Raphael and Michelangelo go to Manny's Meats, and Donatello and Splinter go to the United Nations Building. When they reach those locations they discover that the Keystones are guarded by Keystone Wardens. The three groups manage to defeat the Wardens and take control of the Keystones, which begins pushing back Shredder's power. When Shredder finds out, he punishes the Foot Mystic for not telling him, and then activates his dragon power. His intense magic overwhelms the two teams and Shredder captures the Keystones.