Sæson to starter med chokerende afsløringer om Jane Does sande identitet og hendes forbindelser til terrorgruppen Sandstorm. Nas Kamal - lederen af en hemmelig NSA-afdeling - slår sig sammen med Weller, Patterson, Reade og Zapata for at bekæmpe Sandstorm. Med eksplosive trusler på alle sider er det mere presserende end nogensinde før at løse gåden i Janes tatoveringer.

Episoder:
01: In Night So Ransomed Rogue
02: Heave Fiery Knot
03: Hero Fears Imminent Rot
04: If Beth
05: Condone Untidiest Thefts
06: Her Spy's Harmed
07: Resolves Eleven Myths
08: We Fight Deaths on Thick Lone Waters
09: Why Let Cooler Pasture Deform
10: Nor I, Nigel, AKA Leg in Iron
11: Droll Autumn, Unmutual Lord
12: Devil Never Even Lived
13: Name Not One Man
14: Borrow or Rob
15: Draw O Caesar, Erase a Coward
16: Evil Did I Dwell, Lewd I Did Live
17: Solos
18: Senile Lines
19: Regard a Mere Mad Rager
20: In Words, Drown I
21: Mom
22: Lepers Repel