He did a creepy 'reveal' ceremony to his troops where he showed them the true nature of the Headless Monks. He revealed that the Headless Monks are, in fact, headless. Big suprise! At the ceremony, the Doctor disguised himself as one of the Monks and infiltrated the facility. Manton was caught completely off-guard and the Doctor disappeared into the shadows. Since he was disguised as a Monk, Manton's soldiers started firing on the Monks. Having lost control of his men, Manton wailed for a bit and then retreated as his men were massacred by the Monks. As the soldiers finally got things under control, an army of Judoon, Silurians and some other of the Doctor's companions teleported in to arrest them all.
The Failure of a Colonel attempted to escape on his ship, but it was taken over by a group of Pirates hired by the Doctor, and his base's communications were taken down by Spitfires. Defeated, the Colonel was forced to adopt the name 'Colonel Runaway'. What a failure. Oddly enough, Emperor Wassabe I, Destroyer of all that is Good wrote a definitive history of Colonel Runaway and his allies, and made up a complete lie that he teamed up with some creepy eye-patch woman called Madame Kovarian, and that the Doctor only came to the base of the Church to rescue some redhead. W-E-I-R-D.