Love is in the air in Eureka - or, maybe it's in the microchip, since Fargo has dedicated himself to spending time with the hologram Holly. When Deputy Andy suggests that Fargo get a life, he ominously hints that he and Holly might not have as much time as everyone thinks.
Allison is off to a day in a submarine lab in Lake Archimedes, and just as she's settling into the sweet sound of no kids, housemates, or worry, who should appear but Jack. As part of a plan that's been a long time in the making, he sweeps Allison away in the sub and attempts to treat her to a romantic lunch, complete with a virtual Vince maitre d' from CafÃ© Diem. Something's obviously gnawing at Allison, and Jack thinks it might be related to the fact that she hasn't told her family about their engagement, but before they have a chance to really talk about it, the sub gets swept up by a vortex and plunged to the bottom of the deepest trench in the lake. With only the emergency power system operating, Allison and Jack have to hope that someone notices them missing and comes to the rescue.
But the folks on the surface have their own issues to contend with, since pockets of water keep bursting in where they're not welcome - like in Fargo's office, or sensitive experiments, or control panels. Jo realizes that Dr. Fowler, who's been working on a teleportation device, is to blame. All of his transfers of lake water have been leaving - causing the vortex in the lake - but not arriving in the tank, as they should, meaning there's a glitch in his device. Fowler thinks it must be a prank related to Feynman Day (Eureka's version of April Fool's Day), maybe even the prank Zane pulled on Jo when he altered her business suit into a pleather Cat Woman outfit. Zane insists that outfit was targeted to Jo's DNA and couldn't have been corrupted.
Back in the sub, Allison and Carter realize that the virtual Vince can act as a radio to shore, and they quickly send out a distress call, which gets picked up by Henry, Jo, Zane, and Fargo. Time is of the essence, so they'll have to try a risky rescue maneuver: they'll combine Zane's DNA tracker with Fowler's teleportation device, and zap the two back to GD. As the water rises around their shoulders, Allison's cold feet about the wedding get hot. With Henry communicating via radio, she asks him to marry them. He does so, and with a kiss for luck, the newlyweds are transported back to safety.
Things are back to normal for most, but Zane's life is definitely not normal, since he's just been promoted to Head of Sector 5. More importantly, he's agreed to help Fargo find a way to keep Holly, who defies any kind of computer mainframe, safe and sound. She's unstable in SARAH, and Zane is maybe the only programmer out there who could create a framework able to sustain something as complex as a human consciousness.