There are three Nega-Cores, each with its own guardian. The other two cores (and their respective guardians) have yet to be revealed.
IDW comics continuity
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Arcee, in her rampage to destroy all things Jhiaxus, attacked a facility that housed the Nega-Core. Ultra Magnus managed to incapacitate her before she destroyed it, while Jhiaxus' drones informed him that the device was undamaged.
Once the Nega-Core was complete, Nemesis Prime dispatched Cyclonus on a mission to activate the Nega-Core and its guardian in preparation for the Expansion. Cyclonus allowed himself to become distracted by the Ark-12 and barely reached his target in time. He initially planned to ignore his secondary objective, out of a personal distaste for what Thunderwing had done to Cybertron, but was ultimately forced to activate the guardian when Ultra Magnus and the Ark-12 crew followed his trail to the Nega-Core's hiding place.