This scenario captures the atmosphere of the Schism on the ground extremely well and has a real "ripped from the headlines" feel.
2 points that could maybe bear improvement:
- Rather than Puppet Shows/Shadow Plays, at least at the outset it seems similar to Convergence. A Cell might issue the Agents with protomatter detection spray (which probably does nothing, because the avatars aren't Mi-Go protomatter, unless you think the March/Cookbook tech is similar enough to trigger it). Given the kinds of research, links could also be drawn to Viscid.
- An implausible point which struck me is that the police and Arizona State University apparently take little notice of a whole team of scientists who work together all going missing within a week. That strikes me as a national or even international news headline event. My suggestion would be that, as well as setting up a front commercial operation, PHAETON used its access to March/Program/USG computer networks to fake the scientists' collective recruitment to a "top secret" "national security" project which demands on-base residence, maybe using obsolete Majestic-era security protocols from the Ice Cave/Area 51 era. It might be composing AI generated bland emails or faked video conference calls home, ensuring their salaries are still paid, etc. This could add a layer of Schism intrigue if the Program thinks they really are working on a top secret project, and extra investigative leads for IT-savvy agents, or interviewing family who sense that something is really wrong/off/fake about the communications from their loved ones.