Crossover with Xcom.
MESSAGE FROM THEIR ROYAL MAJESTIES-BURN AFTER READING
Greetings Commander, as you are aware Equestria has recently suffered a series of attacks from a force or forces unknown to most ponies. It is with a heavy heart that we must inform you of the activation of the ECOM Project. With the activation of this program you will have access to Equestria's brightest minds,newest and most experimental technologies as well as its strongest and most battle hardened soldiers. My sister Luna and I along with Princess Cadence, Prince Shining Armor, and the bearers of the Elements of Harmony will act as a council that will monitor and oversee the project's progress. Remember Commander that you are currently Equestria's first and only line of defense against these unknown forces and we expect great things from you as a result. Good luck Commander.
Your fair Soveriegn,
Princess Celestia
Author's Note: This is an idea to inspire some battle scenarios that pit the UEE against human or legitimately extraterrestrial forces. Post and give any thoughts or criticisms.

Okay, some specifics

Forces: UEE vs Humans/Aliens (author's choice)

Tech Level: Modern Punk (Conventional modern weapons and tech is available but swords and sorcery is the norm while M4's and RPG's are the exception).

Scenario: You are the commander of ECOM, Equestria's special defense force against threats from beyond the borders and stars as well as any internal "delicate" matters. Each "round" lasts an ingame month and during that month the author of the scenario can have events occur such as abductions, terror attacks, and etc. While these are happening the player is researching tech, carrying out autopsies on retrieved enemy dead and generally doing everything possible to appease the Council.

The Council: Princess Celestia, Princess Luna, Mane 6, Shining Armor, and Princess Cadence; Each council member will have a "Faith Meter" and depending on your success, or failure, during missions as well as running the day to day operations that faith will increase, decrease or be unchanged. It is vital that you appease the Council as the effect of one member leaving can ripple out and change how other members regard you. For example, if Shining Armor leaves then Cadence's faith will plummet if she doesn't leave with him outright and Twilight's faith will drop significantly.

Budget: At the start of each month, the player receives 1000 bits (minus expenses; first month is the exception because it is the start of the game), X Earth ponies, X Pegasi, and X Unicorns which can be assigned to one of three jobs around the base.

Jobs: The ponies under your command can be assigned to any one of three jobs;
Soldier: Fighting Unit that heads out on missions (Recommend: Earth Ponies and Pegasi)
Scientist: Researcher and technician in charge of developing and maintaining equipment. The more Scientists you have the faster research is completed and the sooner the player gets shiny new tech to make baddies go boom. (Recommend: Unicorns and Pegasi)
Engineer: Worker who manufactures items researched by Scientists and does maintainance around the base. More Engineers means increased production speed and reduced cost to produce and maintain. (Recommend (Earth ponies and Unicorns)

Base: Command Center, Situation Room, Research Center, Engineering and Manufacturing Center, Satellite Uplink, Barracks, and Officer Training School.
Structures/ Add-ons:
Command Center: Main area where available missions can be viewed and teams deployed
Sit. Room: Shows map of Equestria and current Panic levels in various areas as well as Faith Meters for the Council
Research Center: Assign Research Projects and develop new tech, weapons, armor, and etc.
Engineering: Build, maintain, and eventually upgrade weapons, armor, and etc.
Satellite Uplink: Allows two satellites to be deployed each, gain an extra satellite for every and any adjacent uplink structure.
Officer Training School: Unlocks perks for all currently enlisted Soldiers such as faster recovery from wounds or less likely to die from a fatal attack.
Barracks: Living Quarters for player's Soldiers
Power generator: Supplies additional power to the base (Base starts off with enough power to run all starting structures plus two additional ones) every adjacent power structure adds two extra Power Units (Increases max power of base for example; Starting Power X/30, w/ generator X/35)
Laboratories: Give Five Scientists upon completion of construction and increase max number of research projects that can be under taken (Can have one research project at the start and gain one additional project for every two Labs built), any adjacent labs add one additional Scientist each ( Two adjacent Labs= 2 extra Scientists)
Foundry: Unlockable structure that allows for purchasing upgrades to current gear.
Satellite Nexus: Upgraded uplink structure that can run four satellites. Complete Research projects to unlock, any adjacent uplinks allow for extra satellite (Author's choice as to what projects)
Other: Any additional structures are up to the Scenario author.

Note; Players must provide map showing layout of their base to avoid cheating by claiming adjacency bonuses everytime a new structure is made. Command, Research, Engineering, Barracks, and Officer School are one time structures that Base starts with and do not have to be built. All other must be constructed and size can be limited by author to avoid structure spamming in order to rack up bonuses.)

Requests: If the author includes them, players can also perform Requests, specific orders given by a Council member ( for example, Fluttershy asks you to capture X number of a certain enemy type in X rounds to recieve X extra bits , X number of Scientists or engineers, or an auto leveled Soldier). These can also restore some of a council member's faith in the player if things start going FUBAR in later rounds of the game, especially if the Scenario author is mean spirited or a horrible sadistic monster bent on ponycide regardless of the player's feeble attempts at resistance.

Also because ECOM is a black book organisation, the player can recruit units and form alliances with other factions that currently exist regardless of whether or not they are mercanaries. For example, want some Changling Deceivers to slit Sectoid throats? Then make a deal with Queen Chrysalis to share the loot or offer some extra staff that you don't need at the time or maybe request some timberwolves from Discord he 'd problably enjoy causing those aliens some chaos. In short, "the enemy of my enemy is my friend" but author has final say on alliances so yeah.

A quick Word on aliens, if used:
They can be the same aliens or the Covenant or xenomorphs. Pretty much aliens work the same way as in the XCOM games, mostly like the reboot/remake released recently, but you don't have to copy and paste the races and types from the game(s) if that is what you mean. Besides if xenomorphs worked in this scenario like they do in the Alien movie series any player ho went against them would be fighting a losing war of attrition unless they started nuking parts of Equestria left, right, and center to insure they were "sterilized" or whatever and Princess Celestia no like mas slaughter of innocents regardless of the reason.
Long answer look up any footage or info related to the new XCOM game and take whatever you want from it (characters, weapons, research project, storylines, etc) and go to town with it. Just try to avoid trolling players during the game by having their good team dealing with a crashed UFO, their decent back-up team responding to an abduction alert while their Bad Company (low-level units) are left to deal with an alien terror attack in Canterlot where stallions are dying all over the place while mares are taken captive and used by the invaders as breeding factories raped daily until pregancy is assured, minds shattered to the point of being vegetative sex dolls that only care about giving birth to some hybrid infiltrator abomination that has no real right to exist and should be killed with fire. But we don't have to worry about that because no one here is that sadistically evil, right?

Finally, does the author have a part to play?
Yes, the author is a lot like a GM for D&D in that they have to keep play engaging by weaving a narrative that takes the player's actions into account as well as any events of significance such as council members leaving or the effect attacks have on Equestrian settlements depending on how much detail the author wishes to get into. Below is a two step quickie guide.
1.Use the materials provided to come up with a campaign and missions/events that will occur throughout either at random or after the player performs certain actions, if there is an overarcing story.
2.GM campaign for any players participating, making sure to note what actions they have taken in order to "save" their progress as not every player will be consistent or make the same choices.

There are some of the specifics they are open to change based on the author's whims and imagination so take what you like, discard what you don't and go nuts!

what the shit am i reading

Equip ever soldier with a rifle and tell them they don't leave base until they can shoot through a flies' ass at 400 meters.