While Evan went to the island to perform a Soul Search on the individuals who came out of the portals, Valery also sought out Leon and spoke with him about what had happened in Antarctica.
She made the excuse that they had gone to Antarctica for a friendly sparring match and it was nothing serious. As for why she had instructed the hunters not to go near the portals that appeared across the Earth, she simply told him to meet with Evan the following day.
Of course, even with Valery's warning, it was impossible for the Federation to ignore the portals that had appeared all over the Earth. So, once the shadow undeads captured the people who emerged from the portals and left, some high-level hunters went there to investigate.
