After Zardoz sends out 3 bogus ships, Jaffra’s team will divide up among two ships and 3 shuttles to pursue Hanaka. Sam and Barnes board a commercial airline with McMillan en route to Chicago. After meeting with Director Holliday, Kate learns more about what Operation Ralph might be. Thornton and Scarlett follow leads in New York and line up possible witnesses to Meredith’s disappearance.

The Mercury is in pursuit of the ship they believe JoMac is in while the Prometheus catches up. Kate and Nelson discover strange markings on the back of the DC map from the bombing. Barnes and Sam are about to board a flight to Chicago following McMillan. Thornton and Scarlett interview one of the people Jon went fishing wish when he disappeared.

An alien ship lands in the jungle and rescues Hanaka and his guard and JoMac is taken prisoner, while the Mercury begins its pursuit. Simon and his team make their way back to the Prometheus to join the pursuit. Barnes and Sam plan to fly to Chicago following McMillan. Thornton and Scarlett continue their investigation of Jon Windsor. Kate and Nelson continue to piece together the map found at the bombing. Kate consults with her Homeland Security boss.

Simon and his crew decipher the message left by JoMac and begin their search. Kate and Barnes trade ideas and theories on each other's case. Thornton and Scarlett arrive in Canandaigua and begin their investigation on Jon Windsor. JoMac discovers Hanaka's plan for their final escape. Sam and Jim along with Kelly recap their case and think McMillan is too clean.

Kate and Nelson go through the debris from the bombing and try to figure out why a map is highlighting bridges in D.C. Hanaka and his guard lock up JoMac as they prepare to make their escape. Thornton and Scarlett have breakfast in Rochester and prepare to meet with the Canandaigua Sheriff's office. Simon's crew decides to go into the jungle and search for Hanaka's vehicle before total darkness from the eclipse. Kelly runs facial recognition to discover shocking news about one of the men in the park Barnes photographed.

Barnes and Sam follow three suspects in an Annapolis park as they appear to be passing on secret documents. Hanaka and his guard are taking JoMac to a secret RAGE hideout deep in the jungle; while Simon’s team follows their tracks while a global eclipse darkens the way.  Scarlett and Thornton are headed to Rochester New York by plane to make the 30 minute drive to Canandaigua to meet with the county sheriff.  In the Baltimore P.D. lab Kate and Nelson piece together burnt papers to find a shocking piece of evidence.

JoMac has been taken hostage by Hanaka and his guard. They are headed deep into the jungle. Thornton and Scarlett meet with a woman in Kingston Ontario believed to be related to Major Meredith. Barnes and Sam observe what could be the passing of secret information in Annapolis. Kate and Nelson sift thru debris from the explosion and find a startling clue. The Mercury crew make a decision on how to proceed in the search for Hanaka.

JoMac finds himself in the jungles of Titan 4 with General Hanaka and his guard with a very uncertain future. Thornton and Scarlett are on their way to Kingston Ontario Canada to meet with a blood relative of Major Meredith's. Barnes and Sam follow McMillan on the streets of Annapolis. The Mercury team patrols Titan City looking for Hanaka and his guard.

Hanaka and his guard disappear and the Mercury crew goes in search after discovering that one of their own is missing. Kate and Nelson ponder how to keep Hernandez from discovering alien technology. Barnes and Sam head for a stakeout as they continue to investigate McMillan. Thornton and Scarlett arrive in Canada to begin their search for the origins of Major Meredith. JoMac awakens to discover that he's where he shouldn't be.

Somehow Ursula boards the Mercury and escaped with two of the three prisoners. Who was left behind? Barnes and Sam follow up on the suspected vehicle in the McMillan case. Scarlet and Thornton get a big break in the Meredith case. The Mercury crew is out on patrol trying to track down Ursula.