According to Intel from Awakening, the Cortex is a tissue sample collected from the brain of an Ancestor. After scanning many obelisks, CIF Team 1 will arrive in the room with the Ancestors and Archer. Archer is holding the Cortex. CIF Team 1 is instructed by Cross to kill Cryptids around these terminals in the room, as the Cortex gets power from the deaths of living organisms, so that a meltdown can be activated. After killing so many, CIF Team 1 will have to activate the Cortex. After the terminals have been filled, the players must grab the Cortex and leave. CIF Team 1 will have to stop at certain checkpoints to drop the Cortex and fill it up again before activating it to disable three forcefields. After destroying the third and final one, CIF Team 1 can run to the exfil point and end the game.
In Exodus, Samantha Cross will task CIF Team 1 to defend it while fighting the Cryptids and Ancestors. Eventually, it can be activated to kill the Cryptids nearby. It allowed Cross and the other members on the rocket to escape to the Exodus Space Station, but at the cost of CIF Team 1's lives.