At the end of TEIF we certainly see cracks and the start of at least one fault line in the core of the Alignment. The Plan isn't still on the rails and the Alignment has now burned- perhaps as fully intended- the second sacrificial world to cover its tracks. Which does raise the question of exactly how it's leadership (and the earlier planners) expected to fully set up and implement the whole scenario of the Alignment operating as a puppeteer set of at least demi-gods from somewhere that made them untouchable as far as the rest of humanity was get?
They hid on and managed operations from Mesa while creating the screen of Manpower, Mesa and various companies. Then they set up a whole hidden system (with almost 99% lack of access or contact with anyone else except for effectively dead-drops to ship out masses of equipment and materials but no people. Now they have Darius and several sets of technology (the Spider Drives, the nanite assassin routines, and pushing humans to what they are considering the next interim step in evolution though genetic manipulation.
But Darius doesn't seem to be quite what they need yet. It is hidden but also dependent on the defense/obscuring of the wormhole leading to it to the Mannheim (spelling) SDF now possibly bolsters by elements of other systems in the RA. Of course this also means that there is significant number of the Mannheim SDF and government etc that are Alignment members that know what they are protecting.
Are they really so confident that they can withdraw under cloaks of misdirection, slightly superior tech and a program of scorched earth in which they mostly get their adversaries to do much of the destruction for them? It's not so much as hunting down a bunch of Hydras, as trying to exterminate mutant termite/fire aints. Killing you is nothing, you're just waste material if you're not useful to them and to be disposed of. But rooting them out when you can't identify them or any of their cat's paws or unwitting co-conspiritors is both tough and dangerous- and very frustrating since you are groping for shadows.
Short of having the core of the Alignment take what they think they need and head off to start a new species and civilization in another part or our or another galaxy, they are just going to have to try and hide more deeply and rebuild their networks of spies and flunks to come back in 50 to 100 years and try to finish the plan. There has to be a more elegant (from a story perspective) plan than that.
