After killing Henry and leaving Hong Kong, Annie went into hiding for another four months. On Covert Affairs Season 5 Episode 1, she returns to Washington D.C. and contacts Auggie.
After passing a polygraph test, she's reinstated to the CIA and immediately gets an assignment when Khalid Ansari shows up in Chicago. This leads to a new mission when terrorists plan a new attack.
Joan heads back to work at the CIA, but with Calder in her old job it's a complicated situation.