@Background Pony #B788  
Ehhh.. Malal does not even exist.

@Saga The Dragon  
>Tirek  
Blank/Guardsmanspam faggot  
>Tau  
Deep striking with drop pods or get Lord Castellian Creed to sneak a Baneblade into the Etheral’s tent.

The Inquisition would not be directly involved.
 
The Inquisition is in place to deal with threats from WITHIN the Imperium, be it a hive world or an army group, they find the threats inside Imperial citizens or military organisations.
 
Once found, The planet Equestria is on would be dealt with either by quarantine (basically ignored and lost in the paperwork) invasion for the resources of the planet(As sentient creatures, ponies would not be considered a resource and be killed en masse), or bombarded from orbit to wipe it out and then quarantined and lost in the paperwork.
 
IF, IF through some stretch of plot, the ponies of Equestria and humans of the Imperium were to begin to interact in any way other than a hail of lasfire, then the Inquisition would be introduced. If there were rouge trade in Equestrian items other than basic food and supplies or if there were ponies leaving Equestria on Imperial ships, then the Ordo Xenos would be the first in line. If Unicorns were teaching humans magic, the Ordo Hereticus would be first up. I only see the Ordo Malleus being involved for the denizens of Tartarus, like Tirek, or for good old ‘spirit of disharmony’ himself Discord.
 
But as others have said, if there were some kind incident with ponies and humans mixing in anything other than open warfare, every Inquisitor even remotely connected to it would assess the information they were given and may choose to involve themselves, or report it to any other Inquisitor directly or to the ‘organising body’ (head office) of their Ordos where it may get sent in any one of a thousand directions, including getting lost in the paperwork.
 

 
PS
 
 
fanfic time.

My official Warhammer lore friend has responded, after much consideration, the answer is “Whoever gets there first and tells the other Inquisitors ‘This is MY case! BACK OFF’ “ and starts flashing their badges, Inquisitorial Goons, and possible Sororitas around.

@Saga The Dragon
 
The Imperium could always just send Blanks out to deal with Tirek. Particularly, Culexus Assassins.
 
Although, a Tau and Equestrian alliance is something I can oddly see happening. Someone needs to make a fic about this.

The funny part is by attacking equestria they may unleash Tirek into the world, who would consume all the magic and possible go on galactic conquest.
 
Are only hope is if the Tau comes and makes an Equestrian Tau Taskforce. For the Greater Good….for friendship!

@Background Pony #FC6F  
What you did there, I see it.

“Would the Inquisition send the Ordo Malleus after us or the Ordo Xenos?”
 
Why would they send the Ordo Malleus after the Ordo Xenos?

@40kponyguy  
Let’s hope it never comes to this^^

It’d be the ordo Xenos, as stated here
 
@Celestia’s Servant
 
But it depends which Imperial forces met with them first.  
A radical Inquisitor may see that the ponies aren’t really a threat, and would probably just use them to get supplies and labor.
 
A more puritan Inquisitor or army group would more likely just treat them as any other alien species and wipe them out.
 
Although it’s possible the ponies in the series are descended from terran horses. There’s far stranger stuff in 40k than magical talking ponies, and the warp can be used to explain away pretty much anything.  
‘It’s magic, ain’t gotta explain’.

Ordo Malleus deals with demons, while Ordo Xenos deals with anything ‘non-human’. So the answer is clear.

any sort of 40k crossover is going to end badly. Warhammer fantasy might go bit better.

@Heterodyne  

 
Plot twist: Discord is Malal/Malice, the fifth Chaos God…hey, the guy IS the outcast god.
 
(Apologies about the first post, hit enter too quick by accident…and i have no clue how to delete or edit it.)

I suspect any Imperium visitors would take one look at Discord and order Exterminatus.

I’d go with Guard units overseen by an Ordo Xenos inquisitor. Ponies are sapient beings from another planet, after all. The Astartes usually don’t get invloved until shit really hits the fan.

Astartes and Guard. The Inquisition would likely want some oversight, but would leave most of the actual campaign to the Imperial military. The specific Ordo involved would really depend on which Inquisitor is closest.

I’d be pretty sure Ordo Xenos would have authority here being that they aren’t human OR horrible entities from the warp.
 
Though I’m pretty sure who ACTUALLY has the job is which ever Inquisitor backstabs, blackmails, and subterfuges enough.
 
_{Buncha crazy bastards
 
Ciaphas Cain was right}

@DungeonMiner
 
Indeed. Truly the most important questions of our time.

The truly important questions.

Either way, Equestria would be fucked.