From Halopedia, the Halo wiki
A subdural pulse-coded emitter was a type of tracking device used by the Office of Naval Intelligence to enforce the Cole Protocol. They were implanted in all UNSC Astronavigation personnel. The emitters were activated by WINTER CONTINGENCY and nullified once the said personnel were aboard a secure vessel or location. The personnel were unaware of the presence of the device and its purpose.
After the declaration of WINTER CONTINGENCY, field officers were required to use the emitters to secure or terminate Astronavigation assets in order to protect the location of Earth and other human colonies.