They were re-discovered by Master Chief. He was taking an unauthorized joyride on a Hyruleian military spaceship, and floating space, there was a "pretty space ring" as Mater Chief put it.
He landed on the "pretty space ring", and discovered it contained aliens. His nanny told him to use the Halo to blow up the aliens, but his mommy told him not to, because it was aimed at Earth. Master Chief listened to his mommy, and blew up the Halo.
It later turned out there were several halos spread across the galaxy. So, Master Chief used his SPARTAN LASER to blow his way into Halo Central, and he blew it up.
He then blew up another Halo, and then his nanny (who turned out to be supreme ruler of the halos) tried to blow him up. So, HE blew HER up.