What the @!#?@! is a Prototype?
A prototype is an initial, representative model of something. Prototype vehicles like ships and aircraft are carefully constructed to test whether or not their designs will function as their engineers intend. Something might have multiple rounds of prototypes as they are tested, modified and perfected on the road to developing the final production model. But in Privateer 2's Tri-System, the word prototype seems to have a distinctly different meaning.
In 2790, the Tri-System military and the Central Intelligence Service (CIS)'s fleets operate an impressive line of battle: the ML4D Salvia-class destroyer, the MCOS Veldor-class carrier, the MDRE Yackard-class dreadnought and the... MCPH Prototype?! It would be unusual for a prototype in the traditional sense to be in active service… and the MCPH is not rare: we see or learn about at least ten of them in the game. What's more, they aren't exclusively property of the military and CIS: one that we see is operated by the Kiowa pirate clan and two were at one point owned by a courier company (before being captured by the Kindred)!
The MCPH is clearly a type of warship. It has a very distinct silhouette with a split hull that separates an off-centered bridge and weapons platform from the main body of the ship which is built around a central flight deck. There is an additional set of docking bays below this section of the ship. The artwork of the MCPH shown in the manual seems to be mirrored, with the bridge island on the port side rather than the starboard as it appears in the game. It seems to have six engines which seems to match the Salvia-class and put it between the Yackard dreadnought (2) and the Veldor carrier (8). Statistically, the MCPH has the same centerline armament as the military's Yackard-class dreadnoughts, six dual mount turret Bs. They are twice as maneuverable (2/2/2 dps) and have a 40 kps higher top speed (160 kps) than the dreadnaughts, but their shields and armor are about 15% thinner.
In the game itself, they are referred to as military prototypes (in flight) or as specifically {shipname} prototypes; Commissioner Wilcox labels his e-mails "COMMISSIONER WILCOX, CYCLOPS PROTOTYPE". Origin's Official Guide to Privater 2 refers to their class as "military prototype" or "mil. prototype". The original UK manual labels them "Prototype Ship" but curiously the updated American version changes this to simply "Capital Ship". The manuals list them as the last military ship while the guide places them between the carrier and the dreadnought. We can confirm that this is not a case of the Tri-System simply using the word prototype to mean something else. Privateer 2's news briefs mention a "prototype Tiger Shark X-Turbo III" ship and there are missions that involve a prototype Papogod systems scrambler ship you must fight AND a pair of prototype Teflo-Weave pants that you must recover!
So what is the MCPH? A common theme among MCPH appearances in missions is that they are often included at the end of CIS-related missions where you must deliver data or cargo or simply report to the police authorities. One is even labeled "CIS Patrol Command". This suggests that they're intended to be command ships of some sort. We don't know much more than this specifically, but we have some theories. One is that it is a cruiser. The pirate clans all operate cruisers but the military and CIS do not. The MCPH would seemingly fit snugly into the order of battle where a cruiser should go, though it would be overpowered compared to its pirate equivalents. The Kindred-captured Messineo Couriers MCPHes are labeled "Messineo Cruiser" in the mission, though the same is used for their captured military transports and destroyers. Another option is that it is another type of dreadnought. The armament is the same as the Yackard-class and everything else is extremely close. The CCN news briefs do mention the existence of an Admiral-class dreadnought at one point.
Finally, and we think this is the most likely story, this is a case of two ships switching places at some point in development. Specifically, the Yackard-class dreadnought and the MCPH. New Crius Examiner - Military Dreadnought asks you to locate a secret military dreadnought and its fleet, which ends up being a Yackard flanked by three destroyers and the Cyclops and then the final mission of the game reveals that Sheila Nabokov CIS flagship is a Yackard. It almost seems like the two roles were swapped at some point, as the MCPH is larger and more elaborate than the Babylon 5-looking Yackard. Perhaps it was meant to be the cruiser and the "prototype" was supposed to be a top secret, top of the line dreadnought you were to discover during the course of the game. Though we can confirm the Yackard isn't brand new: there's a booth entry for E102_020E which confirms that one has been in service for at least seven years.
Below is a quick registry of known MCPH Prototypes, whatever they are for!

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