Strax is just finishing up a scan of the base and says there are no life forms but them and the Silurians. Lorna reminds them of the Headless Monks, who don't register as life forms. Sure enough, one of them is sneaking up behind a Silurian warrior.
The Doctor is still arguing about the baby when he remembers Amy worrying that the baby would have a "timehead." Dorium suddenly realizes that their victory came without much of a fight. "This is too easy. Something is wrong!" The Doctor is still too busy trying to figure out the baby mystery to respond. He wonders why they would want a baby Time Lord. Vastra suggests they want her as a weapon, which genuinely befuddles the Doctor. Why would a Time Lord be a weapon? For being terribly clever, he's also sometimes very blind. Vastra and Dorium exchange exasperated looks. "They've seen you," says Vastra. The Doctor drops into the nearest chair as the horrible realization of it all finally begins to dawn on him. 900-plus years have finally caught up with him. He looks exhausted and defeated. He flashes back on dissecting the spacesuit with River and discussing the very-strong little girl who forced her way out of it.
After Dorium and Vastra go to gather the others together, a view screen pops up at the control panel. Madame Kovarian has called to check in. They discuss the baby. Kovarian calls her "hope in this endless, bitter war." "What war? Against who?" asks the Doctor, still not quite getting it. "Against you, Doctor," Kovarian practically spits.
The Headless Monks quietly go about killing some of the Silurian warriors. Unfortunately, there's a shot of them that pretty clearly shows the actors' faces behind the hoods, which sort of destroys what bit of suspended disbelief there was. The Monks encase the TARDIS in a forcefield and close in on the Doctor's little army. There's some melodic, wordless chanting. "Oh, dear God, that's the attack prayer!" says Dorium. Rory stashes Amy and Melody behind some crates. Amy advises him to let the others die first, to which he replies, "You're so Scottish!" Heh. He kisses his wife and baby, then heads off to battle.