Somewhere in the ship's innards, Quantum pulls out a bunch of plugs.
Engineering. Trip insists he didn't do anything: "Ask your flunky over here -- he's being lookin' over mah shoulder the whole time." The flunky confirms that Trip never left his site. Even if he didn't, could the flunky really tell if Trip did something to screw up the systems? I wouldn't think so -- they don't seem so bright. "This did not happen by accident," Digimon says. No, it didn't -- it's Divine Intervention. Deal with it. Flunky discovers there's something wrong with the EPS manifolds somewhere. Digimon orders Doubting Thomas and Flunky to go check it out.
In the corridors, Flunky says, "It's on the left." Quantum jumps out from behind a corner says, "You passed it!" and blasts Flunky down. Doubting Thomas whips around, weapon out. By playing on his doubts, Quantum cajoles Doubting Thomas into helping him.
Bridge. They still can't find Lyle because systems are down all over the ship. An alarm goes off. May-Ooh-A-THIRD-Line! reports that a convoy of ships is approaching them. Onscreen, we can see four Fleabag ships flying in formation.
In Quantum's secret bunker -- ooh look, there's Cheney! -- Quantum asks what makes the people the Christalien Scientists are fighting heretics. "We believe The Makers created the Chosen Realm in nine days, they believe it took ten," Doubting Thomas says, adding a fair bit of derisiveness into that last part. Whether it's because he thinks it's ridiculous to fight a holy war over such a minor point, or because he thinks the heretics are idiots for adding a day onto their work week, is not clear, but I'm inclined to believe the former. Quantum snorts over this: "For that you've been at war for over a century?" Doubting Thomas doesn't answer this rhetorical question. Quantum tells Doubting Thomas that the EV controls need to be rerouted to Sickbay, but it can only be done from the Bridge, so he's going to teach Doubting Thomas how to do it. Doubting Thomas asks, "Why?" for the benefit of viewing audience. Phlox has synthesized an airborne agent that will neutralize the Christalien Scientist's body bombs, but it has to be distributed via the EV controls.