Well, since this thread has been resurrected and I've had FFVII on the mind a lot lately for obvious reasons, I thought I'd share this. I don't know if I'd call this headcanon, pure fanfiction, or a pitch for a new game, but it's been bouncing around in my head since Dirge of Cerberus came out:
During the height of the Wutai conflict, SOLDIER was a comprised of fourteen units, the first twelve of which each served a particular role in battle and would be nicknamed accordingly, after traditional FF jobs, and each would be lead by a highly decorated commander that epitomizes that job.
The thirteenth unit would be a twelve-man special operations unit comprised solely of the commanders of each unit, only rarely convened under orders from President Shinra. The fourteenth would be a small, confidential black ops unit under President Shinra's direct command that was created following the Mass Desertion Incident, after which he lost faith in SOLDIER's upper command.
Following the cessation of hostilities with Wutai, SOLDIER's already diminished forces are dramatically reduced into a single unified force, to be broken up into ad-hoc units as necessary, and placed under control of the Public Safety Department, with the Security Department taking over as Shinra's preeminent military force.
Some example unit ideas:
1st Vanguard Infantry Unit "Paladin" – Commanded by the resolute Argento, this unit's motto is "first in, last out." As Angeal Hewley's mentor, Argento instilled in him the sentiment that weapons should only sustain wear when used to protect one's comrades, a notion that he in turn tried to ingrain in his own men after taking command of the unit when she mysteriously disappeared.
3rd Adverse Terrain Unit "Geomancer" – A combat unit whose specialty is traversing and fighting in difficult terrain. Due to the recent rampant flooding in Wutai, they often act as combat divers, outfitted with special gear designed for aquatic operations. Their commander was slain during the final months of the Wutai war.
4th Experimental Weapons Unit "Dark Knight" – A combat unit specializing in the application of newly developed arms, commanded by the brash Genesis Rhapsodos. The unit's members wield a wide array of unconventional weapons ranging from scythes to gunblades, and Genesis in particular has pioneered the use spellblades: experimental swords designed to draw out and maximize the power of a permanently integrated materia orb.
5th Guerilla Combat Unit "Assassin" – A combat unit specializing in guerilla tactics and other covert operations, such as sabotage, kidnapping, and assassination. Its members are adept at acrobatics, stealth, and evasion, and typically dual wield small bladed weapons such as daggers and sickles. Their commander was slain during the final months of the Wutai war.
7th Tactical Assimilation Unit "Samurai" – A special tactical unit created to study, assimilate, and undermine the tactics and martial arts employed by Wutai's elite swordsmen. Its commander, the taciturn Sephiroth, would rise to fame after surpassing the legendary warrior Gilgamesh and besting him in single combat, a morale-crushing defeat that Wutai never recovered from.
13th Special Operations Unit "Ragnarok"
14th Covert Operations Unit "Lost Force"
There would of course be others, such as an Aerial Combat Unit "Dragoon," Materia Support Unit "Sage," Materia Offense Unit "Magus," and so forth.
If incorporated into a game, the functionality would be similar to the Turks in Before Crisis or Class Zero in Type-0. Twelve commanders, each with a unique design and playstyle, participating in a variety of missions together and independently, before and during the conflict with Wutai. The story would depict their victories, defeats, rebellions, and the ultimate betrayal, when the surviving members of Ragnarok are killed by Lost Force after uncovering Deep Ground while investigating the disappearances of their comrades.