Fate/Kantai Collection
Disclaimer: I do not own the characters or places depicted below. I only own the madness the mashed them together. If you sue me all you will get is my allergies.
The arrival of the Abyssal fleet in the world's oceans provoked many strong reactions from every group that you could name and many that you have never heard about. The reaction of one of these groups was both utterly predictable while also completely unexpected.
The Clocktower was faced with an unexpected exposure of a portion of the moonlight world quickly severed all possible connections to the Abyssals and later Shipgirls to preserve the secrecy of the rest of the moonlight world. They succeeded surprisingly well and other than a few specialists and those already in the know no one connected the Shipgirls and Abyssals with the possibility of a wider magical world.
While they were doing this they ceded the research initiative on the matter to various individual magi and magus families. These magi failed spectacularly to the extent that no cover up was needed as the Abyssal response left nothing for the general population to find. This combined with the general effect on the world's economy left no doubt that the matter must be research and then dealt with but no one within the Clocktower was willing to be held responsible for the possible result. This meant the task was bounce from department to department until a certain vampire got bored with watching the mess reminded them that they did have someone who not only had proven able to survive otherwise suicidal situations but also had experience with reincarnated spirits. All it would take was some falsified documents and *shutter* funding and they could have someone onsite to get them the information they needed and best of all she did not answer to anyone in the Clocktower so if she failed no one could blame "them".
That is how Rin found herself working in Hiroshima naval base as an expert in exotic energy/crystal reactions on behalf of the japanese government. She quickly proved her worth by reducing the cost and improving the effect of recovery buckets. Rin also brought her significant other/chief Shirou with her which soon gained her a surprising amount of leeway with various base personnel after they tasted his cooking. Between his willingness to help out on nearly everything and his job cooking at the on base cafe Shirou was soon liked by everyone. This even extended to the Shipgirls who either considered him their dense but caring older brother or the local hottie depending on their age much to Rin's displeasure, though it did help cover her work for the Clocktower.
This continued until in the aftermath of a particularly fierce battle both Rin and Shirou noticed a familiar presence and power approaching. Though much reduced in power they could not mistake it for anything else, a Servant was coming. Before either of the could act a figure out a course of action a figure smashed into the returning Shipgirls as they exited the water. The figure was a Lancer going by the spear he wielded to quickly kill the nearby military personnel before wounding several of the Shipgirls and knocking out one of the destroyers. Grabbing the unconscious destroyer the spearman made a break for it.
Unfortunately Lancer moved directly towards Shirou who reacted by firing several traced swords forcing him to drop the young Shipgirl. Shirou then traced another pair of swords and engaged the servant in close combat.
Despite suffering another normally lethal wound (why do Lancers always stab him through the heart) Shirou manages to hold off the servant until the rest of the Shipgirls could bring their firepower to bare finally driving the servant off leaving Rin to try and explain what just happened. Rin was making progress on this until one of the shipgirls noticed that she could see "Steel" within Shirou's wound and wanted to know if he is a ship spirit too.