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The Honeycomb is a giant building in The Yellow Region, which is a parody of The Pentagon from Earth. The entirety of Part 5 Section 1 (aka. Chapter 5-1) takes place in this location.

The Honeycomb is made of yellow-coated steel hexagonal rooms and walls, to make the shape of one giant hexagon. Being in The Yellow Region, each room is edible, bearing the taste of sweetened solid or liquid honey. The Honeycomb is also known as would be the Central Intelligence Agency in CaerulElimo, originating from Earth. Most of the errands done across this public yet privately accessible location is determining possible wars, creating specialized weaponry, and during Generation 6, carrying out the plans of Phantom Flash.

This location is renovated twice in the CaerulElimo series; one time in the middle of Generation Four, and one time towards the end of Generation Five. Generation Six could also count for a renovation as The Honeycomb is fully controlled by Phantom Flash as Part 2 commenced. During this time while PF took control, The Honeycomb had some of its rooms repainted red, yet still keeping the 'honey' aspect of the large building. Generation Four's renovation was done by the Ocean Prince as "a one-time change for a region I do not control," while Generation Five's renovation was done by Duosion Opal, a younger relative of intelligent mind Reuniclus, saying "We definitely needed a theme for the building, even if it seemed childish. Honey, being yellow, was the most optimum flavor."

The Honeycomb was voted by players of CE to be one of the biggest difficulty spikes to conquer in Generation Six for its extreme amount of enemies and one of the very few stealth missions.