I fulfilled the requirements to complete the Cambridge Polymer Labs quest, but I must have done something strange along the way.

I inadvertently killed the Director after getting "hired" by Molly, but before I even started the experiment.

I engaged the defensive systems, which I believe turned Molly and all of the turrets hostile.

I also have the Targeting HUD on my power armor, which I am told can be a problem. It did make Virgil immediately hostile when I showed up to give him his serum, and removing the helmet did prevent that problem.

My results:

Molly is unaffected by weapons or explosions, from me or from Companion Piper.

Molly is hostile and will pursue us out of the Lab if the timing works out against us.

I have the Piezoelectric Armor, but it is Quest-locked and can't be dropped or sold.

I have the chemical reagents, which are also Quest-locked and can't be dropped or sold.

I do wonder if this is part of that bug which makes some NPCs immediately hostile if I use the Targeting HUD on my power armor.

Addendum: I backed up my save files and started using console commands to see about fixing things.

I was able to manually mark the quest itself as complete.

The armor was still quest-locked, and Molly remained hostile and invulnerable.

Using the .kill command did nothing when I used Molly's base or reference IDs.

So I reloaded from a previous save, overwrote the console-command-modified saves, and moved on.