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"Yes, their energy is faint... Hidden near the temples. If time permits, we will find them and destroy them."
During the Second Great War, Emil Narud kept several crystals in the lower levels of Skygeirr Station, and had Tal'darim forces guard them. When Sarah Kerrigan and the Zerg Swarm raided the lab, Izsha detected the cyrstals' presence. Stukov suggested that they destroy the crystals and collect their energy for the swarm.
Xel'naga crystals appear in the Heart of the Swarm campaign mission "Phantoms of the Void." They can be destroyed as optional bonus objectives. Three appear on the map, each providing a level to Kerrigan. They do not appear on the player's mini-map.
One is east of the player's base, and the other two are in the northwestern portion of the map, to the north and the west of the temple north of the player's starting location. Upon attacking them, Tal'darim forces will warp in to defend the crystals.