Essentially for the exact same reasons, actually. So the Doctor puts his glasses on and something something science. There's an engine, and if they stop it, the Cybermen will come, but if they don't, then the bad thing will happen, which I guess is not Mercy going all black-eyed demon on us, but then it doesn't matter, because there's a "power fluctuation," which is... Mercy Hartigan doing her best Bad Wolf impression. "I can see the stars! The worlds beyond! The Vortex of Time itself and the whole of infinity... Oh, but this is glorious!"
Cyber Leader explains she's wrong, because "glorious" is only something you'd say if you had emotions, and she's like, "Totally! I am having all kind of emotions right now! There is so much joy in this machine!" Which, okay, that made me happy. Happier even than the fact that her body -- which she seems to agree on some level is "vile" -- has been changed, that it may be like until this glorious body. According to a mighty working. But whatever, Cyber Leader isn't having it. "Joy is not acceptable!" So she's still strapped down, and the brain-tapioca sort of takes over, so it's like, "Don't you see? My mind is stronger than you ever thought! It dominates, sir! It dominates you!" And they freak out. "I am new. The might of your technology combined with my own imagination... Yes!" The voice changes from the clangy vibrato before to mostly the voice she had before this whole folly was mounted: "There will be a new race of Cybermen. My Cybermen! Logic and strength combined with fury and passion!"
(Oh my GOD, this is exactly like the cat-penis octopus-headed creature. I swear on that guy from Alphabeat if she or the new race of Cyberwankers suddenly has a change of heart due to the power of the human spirit I am going to spit on the floor. I will do it, sir.) So they shoot science vibes at each other and you think she's a goner, but apparently a standard feature of her amazing mind is that it's also good at shooting lasers at robots. From her forehead.
The Cybermen go down in sparks, and there are sparks shooting out of the thing the Doctors have been babbling about, and the percentage of the whatever is shooting up, up, and the assumption is that when it is at 100 whatever percents, all the children will die. So then there's running. Meanwhile, the CyberKing has eliminated all threats to her regency and now has all the remaining Cybermen under her control, because she can do anything in the whole world, I guess. Except chill out.