This one is a crossover, but probably fits here a bit more than the Idea thread for the other series.
In the late 1990s, a number of seers give out prophecies of great disaster (particularly annoying to Harry, because he just witnessed Voldemort's death
yesterday, and now Trelawney says there's some mad conspiracy to
end the world). Studying these prophecies leads the Unspeakables and a few others to Antarctica, where they encounter a Japanese-lead expedition of muggle scientists that have uncovered a bizarre-looking, unusually large sleeping giant, and are getting ready to poke it with a stick, completely ignoring the lesson they should have learned a bit over fifty years earlier. Naturally, they Obliviate and False Memory Charm all the muggles and send them home, yoink the
gigantic bident, rebury the sleeping giant, and hide it with various charms, possibly including a Fidelous.
Elsewhere, SEELE has deduced that there's another conspiracy out there, this one with very sophisticated memory modification technology, and they appear to have taken the First Messenger. Clearly,
they want to be the ones who set off
Instrumentality, to become gods themselves! This is completely unacceptable to the Committee, and so, while doubling down on paranoid security, they make various attempts to draw this other conspiracy out, always through disposable intermediaries (who are frequently disposed of, once they've given the orders to the actual patsies). Generally, it doesn't work, or just results in more agents getting their memories erased. Meanwhile, their servants, witting and otherwise, continue studying the Messenger they do have, in the
geofront under Hakone.
The Unspeakables and their allies, on the other hand, are looking for a
magical conspiracy manipulating and killing these poor muggles, along with studying the bident, and other things taken from the
geofront in Antarctica. Thus the shadow war goes on, each side mostly missing the other.
Around 2005, the Old Men, growing impatient (and deeply concerned and confused as to why the other conspiracy
hasn't set off
Second Impact already), decide to set it off themselves, using the Second Messenger, and hope for the best. Thus, they evacuate the base under Hakone, taking with them a number of samples, proto-Evangelions, and so forth, leaving behind only the large numbers of more disposable personnel, and numerous innocents in Hakone, along with a large number of hidden cameras of various types (though they don't know it, the only ones that will be of any use are not on-site, but looking through miles and miles of optical fiber).
Of course, they don't have the lance, and they may not
know quite how to use Lilith to set off Second Impact. If it fails, completely, they've killed or severely Lilith for no gain, and will start getting even more desperate. If it's partially successful, destroying only the Hakone area (where no magicals live at the time), it won't count as Second Impact (the Dead Sea Scrolls are pretty clear on the level of devastation involved), but it will distract their adversaries, because the number of muggleborns born afterwards will increase a thousand-fold (I would guess that would include the younger sisters of both Touji and Hikari). The other option might be more interesting:
If it
would have set off Second Impact, there would once again be prophecies, Unspeakables and others would invade the Hakone geofront, and they'd be a lot more thorough in questioning the patsies, before changing their memories, and hiding this geofront, as well. This would also cause them to take a close look at the science of metaphysical biology, and realize that the Conspiracy of the Soul they're hunting has been having muggles scientifically investigate magic, and they're
making progress. This is a massive threat to the Statute of Secrecy, and thus they're able to draw in more resources, from several ministries. Everyone researching metaphysical biology must be interrogated, obliviated, and disdredited, and all records destroyed or heavily modified.
SEELE, meanwhile, observes the recordings from the only cameras that did record anything, the ones at the ends of optical cables that several had thought were a waste of money (SEELE 7 gets to be smug at them), witnessing strange people in robes showing up in areas they shouldn't have been able to get to (by sheer luck none of them apparated or disapparated in front of any of those cameras), mind controlling people, and waving around sticks that are probably just props. Clearly, these people are far ahead in the field of metaphysical biology, a theory that seems confirmed when scientists studying in that field suddenly lose funding, or otherwise suffer various attacks, if SEELE doesn't hide them, first. Within a year, the only people working on MPB are the ones SEELE has in hiding. Of course, this isn't over. SEELE won't allow that...
Thoughts?
If enough people wish, I'll crosspost it to the NGE Ideas thread.