I think I get what happens at the beginning.
9 wakes up, has the talisman thing, is found by 2, and they're both attacked by the CatSkull. 2 is taken, and 9 somehow loses the talisman to the CatSkull. 2 is brought to the factory and put in a birdcage while the CatSkull digs out the place where the talisman is put. Meanwhile, 9 is spotted by 5 and brought to the others. It's possible that the Flying Machine attacks then, but I'm not sure. 9 and 5 go after 2, are seen by the CatSkull, fight ensues, 7 shows up and kills CatSkull, 9 is stupid and wakes up the Fabrication Machine, 2 dies, 7 is left hanging in front of the FM.
It also shows that the Scientist may have built that feature into the B.R.A.I.N.-turned-Fabrication Machine as a sort of failsafe, and in order for it to keep running, it needs a sort of "life force". That could be why it's hunting the other stitchpunks down; to get their life for itself.