Even the simplest TARDIS needs to be intelligent just to keep itself whole. For this reason, TARDISes are alive and semi-sentient. The Protyon Unit serves as the Central Cortex Element and functions as the "brain" and "soul" of a TARDIS. The Protyon Unit is located in the Core Service Module and is made up of morphologically unstable living organic matter that takes the form of a massive room filled with billions of organic eyes that wink on and off in binary. The Protyon Unit is made up of a matrix of single-cell binary activators. Each Bit has very limited decision making powers based on the input it receives, however together the Protyon Unit has a mental capacity far beyond the human brain. It works on principles similar to the Matrix on Gallifrey and consists of a nonlinear series of time-frames, which serve as neural pathways. Organic matter is used because only an organic mind can process Block-Transfer Mathematics. The matter needs to be morphologically unstable to adapt to the complex needs of a TARDIS. Some of the few races that can create this type of matter are the Time Lords, Axos, and possibly the Nestenes. Dangerous Hadron Power Lines are used to supply power to block-transfer generators.

A TARDIS can think, but in a manner similar to a machine, not that of a human. As a four-dimensional life form, a TARDIS has casual probabilities instead of thoughts. These probabilities are only capable of replicating the most rudimentary of three-dimensional thought processes. Though, given the opportunity, a TARDIS will voluntarily "talk" to other TARDISes, a properly maintained TARDIS doesn't have emotions. A TARDIS cortex displays about the same amount of mental activity as a Time Lord, but its understanding of Time Lord thought processes is extremely limited (as are the Time Lord's understanding of a TARDIS).

This organic computer processes the Block-Transfer Equations from a TARDIS's Grey-Prints. A TARDIS, and almost everything inside, is generated by these equations. Even an outdated block-transfer modulator (with a few sticky-backed matter augmenters) can create massive (if simplistic) structures. Matter created by a TARDIS using block transfer has enhanced temporal properties and are resistant to being retro-annulled. This also makes it immune to the normal Vortex energies. During the Time War the matter used for the internal structure of a TARDIS can withstand a full-on thermonuclear blast. The Protyon Unit's matter generation technology is used to generate custom designed modules and upgrade modules which are then linked (via space-time bridges) to the Core Service Module. The Protyon Unit uses the raw matter that makes up the walls of the Time Sceptre and unused secondary corridors and rooms to generate new modules as needed. The interior is constantly being reformed and remodeled. The Protyon Unit keeps in constant communication with all parts of a TARDIS using Artron transmissions.

Any object the crew brings into a TARDIS will be replaced with a block-transfer duplicate if left alone long enough. Since it is now part of the TARDIS, this matter can be manipulated and deleted by the TARDIS. A TARDIS can manufacture any substance in practically unlimited quantities. A fully functional TARDIS can create any type of currency including gold (but probably not mercury or Zyton-7). Some (but not all) Gallifreyan technology is made of non-atomic matter. A fully functional TARDIS is prohibited from creating mathematically modelled life-forms. However it is possible, and once created such life-forms can be reconfigured into other "species." Temporal Orbits can even be used to fold time allowing any object or objects to be constructed - apparently - instantaneously.

The Protyon Unit is protected by warning messages and Teleplasmic Minefields, but the TARDIS's Protyon Unit is vulnerable to high temperatures (over 40 degrees Celsius). When the internal environment's temperature rises beyond a TARDIS's engineering tolerances, then the automatic controls will be disabled. Venting the Thermo-Buffer can be used to cool the interior of a TARDIS when the environment is unstable. It can also be infected by creatures like the transmittable Virus of the Purpose - but it will quickly purge its systems with a rather explosive energy discharge in the control room.