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Captain Tom Chandler and the crew of the USS Nathan James set out for the Arctic with two civilian virologists, Dr. Rachel Scott and Dr. Quincy Tophet, who claim to be studying birds. When they come under attack by a renegade team of Russian forces, Chandler learns these virologists are actually collecting samples of the source of a deadly virus that has wiped out over half the human population while they've been at sea. As they head home on the orders of the remaining U.S. government, Chandler and his crew realize that home is a shadow of what they left, and the safest place to develop a vaccine for this deadly disease is out at sea on their ship.

Chandler and his crew head to the U.S. Military base at Guantanamo Bay in hopes of collecting food, medical supplies and fuel replenishments. Three teams are dispatched to carry out these varied tasks. While there, they come under attack by escaped Gitmo prisoners and enlist the help of a grizzled private contractor who's been surviving for weeks and living off the land.

The James faces off against a new foe who demands Chandler hand over Rachel and her research. When Chandler refuses, he and his crew are put to the test as Chandler engages in a series of risky strategic moves. But it turns out their new enemy has his own horse in the race to find a cure for the virus.

Days after a trying series of events at Gitmo, Chandler and his crew are put under extreme duress when the ship's propulsion system suffers a catastrophic event. With Dr. Scott in danger of losing all her research on the virus and a crew overworked, overtired and desperately low on drinking water, Chandler's leadership and ingenuity are put to the test.

With Rachel close to a breakthrough on her vaccine, she, Chandler and XO Slattery lead a small team into the jungles of Nicaragua on a mission to find monkeys for her vaccine trials. While there, they find much more than they bargained for when they run across a former drug kingpin who will stop at nothing to maintain his stranglehold on his oppressed society. Chandler and his men find themselves in a huge moral dilemma over whether to eliminate this menace or take what they need and continue on with their mission.

After returning from the horrors of Nicaragua, panic begins to spread throughout the ship when Lt. Danny Green comes down with a mysterious illness that could be the virus. Losing faith in Rachel and her failing vaccine trials, Chandler now has to deal with a restive crew. If he fails to keep the crew together, the whole mission is in jeopardy.

After picking up a distress call near Jamaica, Chandler and a small team stage a rescue attempt. But a surprise attack leaves Chandler and Tex stranded at sea. Slattery and the crew search desperately to find their lost at sea Captain and his comrade, hoping to do so before their enemies beat them to it.

With Chandler and Tex caught in a dangerous situation, Slattery has to step into the role as commanding officer. Torn between a mission with the fate of the world at stake and a Captain in danger, Slattery has to find a way to get his people back without losing the most important asset: the vaccine prototype.

Rachel and Chandler ask for six volunteers to participate in human trials of her vaccine, but the tests could be a living hell as the virus and the vaccine do battle inside their bodies. Meanwhile back in the States, Chandler's wife and father are doing everything they can to keep their family alive.

Chandler and his crew finally return home, where a former D.C. power player is fending off a dangerous warlord who threatens everyone's hopes of restoring law and order in society. Now with a location and a means to finalize their mission, Chandler sets out to find his family, only to discover something absolutely terrifying about this brave new world.

After the horrifying revelations and reversals of fortune in Baltimore, Chandler and his fractured team join forces with an underground resistance in an attempt to defeat Amy Granderson. With doses of the cure running low, Rachel tries to do some good for the sick while remaining a prisoner at Avocet. Meanwhile, Slattery and the crew of Nathan James are in a race against time to save an injured Dr. Tophet and regain control of their ship.

Rachel tries to help the sick while remaining a prisoner; Slattery and the crew try to regain control of their ship.

Nathan James returns home to Norfolk on a mission to produce and mass distribute the cure. With his family now safely aboard the James, Chandler sends his crew in search of their own friends and loved ones. Who, if any, will find their families? And will those who do return to the ship?.

The crew of Nathan James discovers that hospital ship USNS Solace was sent to sea to wait for Dr. Scott's cure. Captain Chandler sees an opportunity to add another ship to their fleet while Rachel is eager to find a lab better equipped to replicate the vaccine. When Solace fails to respond to radio communications, Chandler and his team board the ship..and come face-to-face with an unexpected enemy.

With a small group of survivors from Solace in tow, Chandler and his crew square off against an enemy of the most dangerous kind - a nuclear-powered submarine led by rogue British naval officers, Sean and Ned Ramsey. XO Slattery interrogates a captured mercenary from the hospital ship in an effort to extract information on the sub and its mission. As Nathan James engages in a perilous game of cat-and- mouse, the truth about the mercenary sub unfolds.

Chandler tracks the immunes to Northern Florida; Rachel comes across a secret formula that her mentor was working on; Chandler's team locates an immune compound.

Slattery struggles to evade the sub; Chandler and the land team infiltrate the immune compound; Danny discovers that Niels is working for the Ramseys; Chandler manages to encroach Sean's inner circle.

While trying to piece together Dr. Hunter's lost formula, Rachel deals with the fact that her sworn enemy is on board the ship; Chandler tries to reverse the brainwashing Michener suffered at the hands of the Ramseys.

With Dr. Scott on the verge of a breakthrough, Chandler and his team set out to land in search of much needed supplies and materials for her lab. Once there, Burk stumbles upon a gang of children who have been offered a bounty by the Immunes for information on the U.S. Navy. A vicious battle ensues when the Immunes come to collect their prisoners. Back on the ship, Rachel's efforts to produce a spreadable cure depend on Niels - her success now inextricably linked to the scientist who nearly erased mankind.

Rachel is hard at work on a new, more efficient version of the cure while Alisha decodes a message found on a cell phone recovered from the Immunes on land. A suspicious death on the ship forces Chandler to launch a murder investigation, causing dissent among the crew and threatening to upset good order and discipline. Armed with new information provided by Michener, Nathan James heads to New Orleans, only to find that the Immunes have a terrifying surprise in store for them there.

Sean Ramsey broadcasts a message implicating the Navy in a devastating disaster. It's now more important than ever for Chandler to infiltrate their network and regain the trust of the American people. Nathan James locates the source of the Immune's signal - a mysterious oil platform in the middle of the ocean. Once there, Chandler and his team engage in a brutal battle with civilian forces who have aligned themselves with the Ramsey's plan.

After retrieving the mastermind behind the Immune communications network, Nathan James finds itself trapped between the sub and civilian blockades set up by the Immunes. Chandler sends Dr. Scott and the cure off the ship under the protection of XO Slattery as the James heads towards its inevitable final showdown with the sub.

With their mission now fully dedicated to spreading the cure, Nathan James puts a call out to civilians to meet at pre-selected ports across the country, where all will receive the cure. However, small Immune factions remain active in their quest to fight the cure and fulfill Ramsey's dreams. Will Nathan James regain America's trust? Has the havoc and destruction caused by the Immunes ended all hope to spread the cure? Or will Nathan James prevail against the enemy and finally spread the cure?.

CNO Tom Chandler is sent to Asia to investigate a possible mutation of the Red Flu. Captain Slattery and his crew deliver cure to Southeast Asia but there may be an unexpected threat in the region.

Chandler must find a way to return to his old crew and investigate a dangerous new foe.

Chandler and crew race to find answers in an Asian Dodge City. Slattery begins to unravel the truth about his troubling predicament.

Chandler must confront his suspected new foe. Slattery learns more about the supposed virus mutation. Pressure mounts on President Michener as the situation worsens

Chandler's mission becomes complicated as his position is worsened. President Michener faces pressure from the regional leaders

Chandler's mission comes to a head as he prepares the final part of his plan. President Michener ponders the fate of his presidency.

The Nathan James must evade an overwhelming threat. A revelation in St. Louis puts President Michener in a terrible position.

America copes with tragedy while Chandler further investigates the possible virus mutation.

Chandler gets a lead that could help answer threatening questions. Kara does some digging in the White House.

Chandler finds himself faced with a difficult decision when a strange order comes in from the White House.

Chandler comes face to face with his powerful enemy in a final showdown. Kara joins up with someone that can help with her mission.

Chandler returns to America to find out what has really been happening.

The fight for America comes to an end; Chandler faces a challenge that could change his life forever.

Sixteen months after thwarting the coup in America, Nathan James must face yet another global disaster. The question remains, where in the world is Tom Chandler?

Having lost their only lead, the crew of Nathan James continues their search for an item that could save the world. Chandler immerses himself in a mission for revenge.

Nathan James's crew searches for a precious item leading them to a strange place of opulence and violence where they cross paths with a most unexpected ally.

The crew searches for one of their own as enemies close in on all sides. Slattery is haunted by visions of the past.

Nathan James is diverted from their mission when they receive a suspicious distress call from a fishing trawler.

With an enormous storm on the horizon, Nathan James must navigate an equally terrifying threat in order to make it to safety.

The search continues with a reconnaissance mission but things turn violent when an old foe resurfaces.

An undercover mission in the land of the dead leads to disturbing revelations about Dr. Vellek's sinister plans.

The crew of Nathan James faces a threat that will test the limits of their Naval tactics and strategies.

Chandler confronts his enemy — and his personal demons — in a final showdown, with the fate of humanity on the line.

Three years after overcoming the global famine, the United States Navy is ready to unveil its first fully functional fleet since the Red Flu pandemic, but a new type of threat may mean the next world war.

Thrust back to World War II era military technology, Nathan James must think fast to survive a fight with limited weapons capabilities.

With nations being rapidly occupied, Chandler tries his hand at diplomacy to unite two hostile countries so they can fight a common enemy.

As Nathan James and her allies attempt to prevent the enemy moving north, Chandler's haunting visions manifest into reality.

After months of fighting, the crew of Nathan James must embark on a dangerous mission to secure important intel that could decide the fate of the war.

Nathan James must seek the aide of a prominent rebel leader in order to create a staging area before mounting an invasion of their own.

Pinned down after days of fighting, Vulture team must find their way into a secretive enemy camp.

With a devastating hostage situation occurring back home, Chandler must devise the perfect plan to avoid losing everything.

The crew of Nathan James begin preparations for what may be their most ambitious mission to date.

It is all out war as Chandler must face his fears and confront the greatest threat he has ever encountered.

Series finale