I had an idea along these lines, but I cannot write decently, and lack the needed background for pulling it out.
An Abyssal attacks a local tribe in South Africa, and the shaman/mage/witch doctor/whatever they're called asks the gods for help and protection. And the gods answer by bringing a shipgirl that destroys the Abyssal ship. The summoned girl is pure African native, but she holds the spirit of one of the RN ships stationed at South Africa to defend and protect the Cape of Good Hope. Once the threat is dealt with, she turns back and presents herself to a young man, calling him "Admiral".
We're talking obviously about a man with no military background, just a hunter or peasant, but the girl sees in him the potential for grasping advanced naval strategies and tactics, so she stays and starts teaching him what he needs to be a good CO.
Time passes, and the rest of the world reacts and organizes themselves against the Abyssal threat. And once they make stock of the global situation, they realize that the South African pass, which should be a key target for Abyssal incursions, has basically very little enemy activity. There is a joint base under South African Navy command, but populated by British-summoned shipgirls, but they only make regular patrols that barely see any Abyssals. Also, when the Brits check their records, they realize that several ships that were stationed at South Africa at one point or another back in WW2 have not been summoned. The mistery is solved when they decide to make a thorough reconnaisance of the shores and find a makeshift naval base holding several shipgirls (no more than ten, and I'd say that six should the right number) and protecting the area against Abyssals.
This raises a lot of interesting issues, as the shipgirls don't recognize the South African government as valid, but they do pledge their loyalty to the Queen. The fact that they are under the command of a civilian with no official training in naval warfare makes things even more confusing.
This scenario could happen either in the Atlantic or Indic coast of South Africa, but I don't know which area is the more likely or appropriate for locating the base, among other things I don't know about the area.