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The Whateley Academy aims to present the façade of a common boarding prep school housing common students, while in fact offering decidedly uncommon classes for uncommon students. An essential part of this strategy is keeping a lot of things underground, in an extensive and elaborate system of tunnels.

The original school already had the seed of this system, in the form of narrow facility tunnels linking the outer buildings to the central campus. At the time the school was built, it made sense to have a central facility supplying steam for heating to all buildings, for instance. Many contemporary schools have similar tunnels. Those are too narrow for regular foot traffic, however. These facility tunnels are still used, although nowadays they also house electric and fiber optic cables for power and data.

Some of those tunnels have been greatly enlarged to offer an underground path from the cottages to the central campus and the Doyle Medical Complex. Originally, only the three farthest cottages, Hawthorne, Twain and Whitman, were accessible by tunnel. The reason is that those are the cottages that house students unable to pass for baselines, who therefore need the tunnels to avoid being seen on red flag days. In November 2006, a spur was built from the Hawthorne tunnel to Poe, which means Poe might receive GSD students in the future.

Beneath the central campus there is a veritable rabbit's warren of tunnels, descending deep into the bedrock under the school. Most of the student labs, where devisors and gadgeteers study and develop their projects, are underground, as are part of the research labs and powers testing facilities. Also of note are the three combat arenas, Arena 77, Arena 91 and Arena 99, all underground. Those tunnels seem to have been dug without much forethought and are laid out in a very complex way, making it easy for an uninitiated to get lost.

Besides the official teaching and research facilities, the underground complex houses many student hangouts. The Cape Squad, the Bad Seeds, the Alphas, the Underdogs and the Lit Chix all have their own underground "clubhouses". The tunnels are so extensive, in fact, that there are entire branches that haven't been used in years, and are sometimes discovered and used by students without official permission. Some students even manage to make their own unofficial "extensions" to the tunnels to house unauthorized "secret labs," to the point that not even the school administration knows how big is the complex.

Digging such an extensive underground network, particularly without disturbing the buildings above, would be probably unfeasible without the help of mutant powers. Fortunately, Whateley being a school for mutants, these are not in short supply. For instance, the very large Arena 99 was built as a student project -- a Senior Legacy -- with no official help from the school. Of particular note in the history of the tunnels is the former student MoleFinger, who had the ability to quickly and easily dig tunnels.

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