The agents manage to deactivate Warehouse 2, but realized it was all a machination by H.G. in an effort to locate the Minoan Trident and start another ice age (reason: She was bitter over the loss of her kid).
Myka talked H.G. out of creating an extinction event, and H.G. turned herself over to the authorities. Ashamed for trusting H.G., Myka resigns because she fears similar judgment errors would keep her from being a good agent.