[Wrote this before DS3, ending is probably not canon, but I had to modify the canon to integrate ponies into the storyline]
It is 2508. The USM Valor is armed and authorized to "rescue" USG Ishimura from the grasp of the Marker. Numerous cases of dementia start to appear in the crew members of the Valor along the journey to the Aegis system, especially in the Marine veterans onboard who have survived the horrors of the Resource Wars and colonial insurrections.

Meanwhile, across the universe, the Royal Sisters of Equestria funded a project to seek other sentient beings in the universe that have been directed along a path of havoc and destruction by Discord. Pinkie Pie, one of the "early-detection" staff, is accidentally transported onto the USM Valor around the time the destroyer's crew begins to experience its final moments, as they find something extremely foreign in one of Ishimura's escape pods....

One of the military personnel that had been deemed a Section 8 onboard the Valor soon narrowly escapes his demise, and, skating on the thin ice of his already broken sanity, meets the aformentioned pink pony in the blood-drenched decks of the crippled Valor.

To join is to survive, and in pieces we scatter.

BTW, it's a non-Isaac Clarke perspective