Xcom: Equines Unknown
By Oubliette

20 years ago, the Ethereal Temple Ship was destroyed by the brave SpecOps troops of Project Xcom. Six months later, Xcom was approached by a party of aliens bearing tidings of not war but peace. The death of the Uber Ethereal and the fall of the Temple Ship had freed many of the alien races from the mind control networks of the Ethereals. Xcom took in these new arrivals, serving as both diplomats to and guardians of Earth's newest residents. Now, though, something new is on the horizon…
A squad of elite troops vanishes through a space-time rift, ending up in a place that they never could have expected.
Equestria.