As Intel documents reveal, children were sedated and brought down to the labs for experiments as a part of Project Paragon and then treated with drugs to induce amnesisa so the children wouldn't remember ever being in the labs. However, one Intel points out that the drugs weren't perfect, as some of the children began to recall the experiences and to associate them as nightmares.
It is unknown what the Abominations were used for, or how they got there as they are too big to be children. The facility also contains an advanced weapons research lab where weapons such as the Armacham Type-12 Pulse Weapon were developed. Terry Halford, one of Armacham Technology Corporation's employees, has an office within the facility.
Their employees are most likely among the dead found throughout the facility.
There are two known ways to enter the facility, one of which is the elementary school nurse's office, which leads down into a monitoring station; and the other is an access route found by going through one of the school's side entrances and through a mock-up classroom which leads to an elevator. This elevator goes down into what appears to be either a lobby or lounge area for Armacham employees.
The unknown deceased in the Paragon Facility are primarily seen in body bags, or skeletonized. Though there is no way to know exactly what they look like, there is a possibility that they have a similar appearance to the Harbinger doctors. One example is in the room with the amplifier, among the dead are doctors.
The filled body bags can be any number of things, one possibility is that they can be employees unfortunate enough to get caught by Richard Vanek and his men. However, it is unlikely that the Black Ops Soldiers would have put them in body bags, as their mission was to cover up evidence and kill people who are related in any way to Alma Wade or Paxton Fettel. Another possibility is that the bags could be filled with ATC dead, possibly wounded and brought down from the battle at Wade Elementary School against the Replicas.