Episode 1 : Lost
After the Astraeus mission?s premature launch to Titan, Allison and the frantic crew manage to land the ship safely... only to find out they are actually back on Earth! But what seemed like only a few hours was in fact a few years, and now the crewmembers have to re-adjust to life as usual back in Eureka, but there?s nothing usual about it.
Episode 2 : The Real Thing
Carter, Henry, Kevin and the rest of the town continue to search for the missing Astraeus crew. Kevin?s strangelet detector discovers the ship?s trail! But where they are and who has been hiding them will be a shock to everyone.
Episode 3 : Force Quit
The ship is finally found but the crew has been taken. When Carter is tasked with attempting to rescue the kidnapped crew by following them into the virtual Eureka, will he be able to get them out before their matrix world collapses for good?
Episode 4 : Friendly Fire
With life back to normal, the Astraeus crew struggles to overcome their Matrix Eureka experience: what was real, what wasn?t and what could become self-fulfilling prophecy. Fargo struggles to come to terms with Holly?s death. Allison and Zane begin to look at their romantic relationships through the lens of a potential future that saw Carter and Jo together. And old animosities erupt as Parrish?s latest pet project literally lights a fire under everyone and threatens to ignite the town.
Episode 5 : Jack of All Trades
The Astraeus crew must move forward after their matrix ordeal, but it isn?t easy. And a return visit from DOD psychological assessor Warren Hughes just adds to the pressure. The emotional fallout and strange accidents along with some bizarre behavior from Carter and others have to be kept under wraps. But when Carter?s life hangs in the balance the unusual activities are revealed, risking the very existence of the team.
Episode 6 : Worst Case Scenario
To better protect against potential security breaches, Henry implements a disaster preparedness drill for Global Dynamics. But the real-life simulation proves a little too disastrous: it may be just an exercise but those missiles pointed at Eureka are absolutely real! Meanwhile, Fargo enlists Zane to undertake a secret simulation of his own-- and faces a hard reality.
Episode 7 : Ex Machina
As the town of Eureka holds a memorial service for Holly Marten, Fargo and Zane secretly work to retrieve Holly?s "consciousness? from the Matrix Eureka computer mainframe. But with the installation of a new "Big Brother" DOD security program at GD, that isn?t easy. Especially when strange hauntings begin to happen at GD, seemingly tied to Carter gaining new "powers".
Episode 8 : In Too Deep
Allison and Carter?s engagement hits rough waters when Carter?s attempt at romance traps them at the bottom of Lake Archimedes in a leaking sub. Their survival depends on Jo?s ability to sort through a series of pranks at GD, Eureka style, and an experiment gone terribly wrong.
Episode 9 : Smarter Carter
When Allison?s genius older brother comes to meet her new husband, Carter feels the pressure of not being smart enough to measure up. But when his intelligence begins to suddenly grow exponentially, Allison has to find out why or risk losing the man she loves for good.
Episode 10 : The Honeymooners
Carter?s best-laid plans to give Allison a romantic honeymoon are thrown for a loop when their definitions of "romantic" differ... greatly. But there?s more in the way of their relaxing getaway when saboteurs are uncovered in Eureka and the re-embodiment of Holly encounters some technical difficulties that could threaten her very existence -- virtual or otherwise.
Episode 11 : Mirror, Mirror
When Grace?s spying is revealed, mistrust is in the air. Major Shaw shows up to take control of the situation just as a geo-engineering project cuts off communications to the outside world, and a mysterious message to Holly has her acting not like herself. But she?s not the only one...
Episode 12 : Double Take
It?s Invasion of the Body Snatchers, Eureka-style. The Smart Dust control unit is still on the fritz and wreaking havoc on the town?s communications systems. Worse, the bio-printer has gone missing, Holly (Felicia Day) is definitely not herself, and Astraeus crewmembers are mysteriously disappearing at the hands of Carter and Deputy Andy.
Episode 13 : Just Another Day...
The DOD is pulling the plug on Eureka. Everyone is processing what do next when the movers arrive early. As Fargo fights for more time, a prematurely packed quantum field stabilizer causes wormholes to randomly appear around Eureka. And as our heroes grapple with saying good-bye, they have to work together one last time to stop the bizarre anomalies before their beloved town is turned inside-out.