Chuck and Hannah unexpectedly become part of agent Daniel Shaw's latest mission. Much to Sarah's chagrin, she gets paired with Shaw, who seems to be trying to get close to her. Meanwhile, Morgan and Ellie continue their mission to get to the bottom of Chuck's secretive and strange behavior.

When Colonel Casey's former team returns looking for him, Chuck must decide what he's willing to sacrifice in order to find his mom. Elsewhere, Morgan works up the nerve to reveal a potentially dangerous secret to Casey.

Chuck and Sarah must race against time and a ruthless spy Robyn Cunnings, to destroy a dangerous computer virus. Meanwhile, Ellie and Awesome are spending their date night which takes on a dangerous turn and Morgan is sent on a special mission to recover Chuck's P.A.N.T.S.