Jo is still having trouble adjusting to the facts she's learned about her alternate self, and things get more awkward when she has to team up with Dr. Taggert to figure out why random things in the town (like a cow) are starting to liquefy. Carter's Jeep is also a victim of this, and Allison figures out that a super acid is the culprit. But where is this acid coming from?
Taggert confesses that his contribution to the Titan mission might be the culprit. He bred bats whose guano could be used for fuel. However, the guano mixed with some chemicals from a tank near the bats' home combined to create the super acid.
The acid causes the FTL drive to malfunction, sending Andy to Titan. And now the team has to figure out how to get him back before he breaks down permanently. The bats also cause havoc in Carter's home as the acid melts down bits of SARAH's wiring.
Allison sends Carter on a mission. In order to fix things in Eureka, they need a full-grown female bat. Carter and Taggert hunt down the bat and things start to get back to normal. They retrieve Andy from Titan and he's reunited with SARAH. As Carter watches the touching scene, he's encouraged to invite Allison and the kids to move in.
Zane and Jo are still working through their relationship, which has soured since Zane found out Jo removed his name from the list of mission candidates. He confesses that he'll miss her and he hopes she'll wait for him until he returns. Jo still isn't sure how she feels about him, but Zane appreciates her honesty.