Following its accidental launch the Astraeus returns to Eureka and the crew discovers four years have elapsed in an instant. The crew quickly learns leadership has changed, procedures have changed and relationships have changed while they were gone and none of it for the good.

The town comes together in a final attempt to locate the lost Astraeus.

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?

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.

Warren Hughes makes one of unexpected visits to evaluate the Astraeus crew. Unfortunately his evaluations coincide with crew members' tendencies to swap minds with Jack. And some of the swaps happen during amorous activities that further stress the relationships of the crew's lovers.

A disaster simulation causes a disaster. Then another. And another. Fargo finds Holly in the computer.

Fargo is convinced that Holly is still inside of the Matrix computer, but the DOD is determined to wipe its hard drive clean -- losing Dr. Marten forever.

Eureka celebrates Feynman day with a plethora of practical jokes. While mostly harmless the jokes make it challenging to identify the real catastrophes Eureka is so prone too.

Allison's also brilliant brother visits the newlyweds to give Jack a hard time but Jack's intellect rises to the occasion. Henry and Zane work on freeing Holly from her virtual reality cage while struggling just to keep her alive.

Jack's idea of a romantic honeymoon doesn't quite mesh with Allison's. Holly tries on her new body. Jo and Andy followup on an investigation begun by Jack's predecessor.

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.

The Smart Dust control unit is still on the fritz and wreaking havoc on the town's communications systems. The bio-printer has gone missing and Holly (Felicia Day) is definitely not herself.

Wormholes cause trouble on moving day. Or is moving day causing trouble with wormholes? While Jack tries to fix the wormholes Fargo is determined to something about moving day.