Nadia Sinh held a big secret during the many Citadel flashbacks we saw from before the agency fell, but unlike what we're initially hinted at, it's not that she was the spy.
Instead, it was that she was pregnant with the child of her and Mason Kane. Before Citadel fell she ran away to Valencia to have the child and nurture it, but eventually she left the kid in the custody of her dad to return to the agency.