He does not appear to be a kill everything type.
Put the Contact in Cheryl, she's likely the one with the least knowledge. Keep her as in the dark as is faesable, and occasionally ask Cheryl to talk to Igor for us.
We need to find a way to look into the chambers and see how the Shoggothim have been altered. It's likely this is a Shoggoth holding lab and the shoggoths here are at least relatively tame.
I suggest waiting for the Basic Report.
prepping the Cheryl.
Asking the Farseers how tangled the Skeins are.
Sending BLU, the Observer, the Droid, the MI and the Prawns out on scouting missions to see if there's anything else around the complex.
Having any dropships currently present in Antarctica see if they can return to orbit or not. If they can't, have them derp around Antarctica looking for reality distortions or the remains of Peabody's expedition.
No combat in the elder lab until we have the basic reports.
UNIT and SCPs guard the World Pillar.
I'd like to get the X-com Psi vets, Tosh, Char, the Farseers, Aurors, Psions, KI Silencers and Cheryl in on a "Let's put Psi in Cheryl" training seminar.
As for the rest of our forces?
When Cleanup's done in Japan, we should get everyone in the Overlord ready to drop.
It might even be worth sending Darius, Star-Lord, Lyla (+ warm weather gear) and whichever KIs can fit in our smallest dropship down at the moment.