There's no such thing as the dead of night in Polaris Institute.
I have a feeling this is gonna change.

With a whistle, he unclipped his ID from his pocket and swiped it through the slot in the side of the lock. It whirred and pushed a pad downward, prompting him to press his thumb against its metal surface. Then, the lock beeped, chirped a greeting, and clicked. Without hesitation, the janitor pushed the handle downward and swung the door open.
It might be just me, but it seems odd that the lock for a lab that was just ravaged still works normally.

Inside, he was greeted by one sight he never thought he'd see. An entire team of scientists, twelve in all, lay on the ground in front of the rows of computers on either side of the room. All of them were either dead or unconscious; he couldn't even tell which. He took a shaking breath and stepped backwards as a cold feeling formed in his stomach, but before he could go any further, two pairs of hands grabbed him roughly. Looking to both sides, he found the faces of two interns – two large ones, much bigger than he was.
This is a GREAT "oh ****!" moment. Good job.

Looking forward, he watched as Professor Nettle walked out of a corner he couldn't see from his place at the door.
There's the other "oh ****!" moment.

"Let's make it so he can't talk, then," Nettle replied. "Jynx, use Lovely Kiss. And you—" She nodded to a third intern, standing at one of the machines. "—contact 009. Tell her our leader will have to be content with two specimens of XP-494B."
Okay three. Stop pulling these surprises on us! XD

The ice witch swayed her hips as she walked towards him. Her pursed lips began to glow bright pink, and she purred as she leaned in and grasped his chin with a large hand. He felt her strong grip clamp down on his jaw, and as she forced him to turn his head, he winced as pain stabbed at his neck. However, he didn't have much time to protest because in the next second, he felt her cold lips against his skin. Shortly afterwards, a tingling, numb sensation spread through the rest of his head, and he suddenly felt like he couldn't keep his eyes open.
Great description of Lovely Kiss.

Helpless inside his own mind, Bill could only watch his body move as if it wasn't his. It thrashed. It screamed. It struggled desperately as Nurse Joy's team of chansey tried to restrain it. Between these moments were gaps in which he sensed morphine crawling through his veins or watched his bones crack and reassemble.
This is a beautiful description. Considering I also just saw a movie with a transformation sequence not too unlike this, I can picture it really well.

This fic is really stepping up, and you're proving my initial impressions of it totally wrong. Excellent work.