After they obtained a fragment of Vartox's axe, Vasquez and Alex Danvers used the obtained info on the object to hunt Vartox. Vasquez later informed "Hank Henshaw" that she found the Valeronian, on his way to National City. The director sent Supergirl to dispose of Vartox, and Vasquez watched.
Red Tornado accident
Exposure of J'onn J'onzz
When Hank Henshaw was revealed to be an alien named J'onn J'onzz, he was taken away for questioning. When Kara asked Vasquez to shut down the dampening technology used to prevent her from eavesdropping, she apparently refused, but Vasquez deliberately left her post open, so Kara could listen in.
White Martian infiltration
Vasquez was there when the base was locked down by J'onn J'onzz. She and the rest of the agents had to figure out who was really a White Martian. So she held her hand out to the fire and proved to everyone that she wasn't really a Martian.