Numerous dissection and drilling tools used in the chimera creation process can be observed here. In fact, the building itself is a chimera, with a strange animal head seemingly fused into the front. In the farthest reaches of the facility can be found a storage room for various people and animals who have willed themselves to the scientists to be spliced in the future, some of which reveal themselves to now be having doubts.
The Chimera Laboratory is visited after a Pigmask mistakenly mentions the outpost to Lucas via transceiver. Upon the party's arrival, Lucas is assumed to be a part-time worker, and is ordered to dress accordingly. He is assigned to find two monkeys (Salsa and Samba) that are running amok about the facility, which he is successful in doing, but is ambushed by an Almost Mecha-Lion which has also been set loose. After besting the chimera, Lucas and Boney must resume their capture of the two monkeys, but is first warned by a Pigmask of an even more dangerous chimera that the monkeys had let roam the laboratory's corridors, the Ultimate Chimera. In a cutscene, the Ultimate Chimera starts hunting Lucas and Boney (with Dr. Andonuts mustering his courage to come nearby and tell them of the power button on its back), knocking their masks off as they flee. The Chimera gives chase, but Salsa, remembering the help Lucas gave him three years prior, saves him by pressing the switch after Dr. Andonuts tells Lucas to use the dog as bait, deactivating the Ultimate Chimera before it attacks Lucas. Dr. Andonuts decides that he is going to leave the military and dedicate his life to making all living things happy, then is chased by a still-angry Boney.
- The Lab's storage room contains EarthBound references such as Dr. Andonuts himself, the book "Overcoming Shyness", and the story "My Secret Life, chapter three".
- The Battle Memory text for the Steel Mechorilla says that it is "A construction Chimera designed to destroy the old Chimera Lab to make way for a new building." Whether this is the old lab that was not yet torn down or the new lab is unknown.
- The music for the Chimera Laboratory is similar to that of Osohe Castle. However, it's played using a different instrument.