This story is a sequel to The God Empress of Ponykind
A message rings through the Warp: "The Game is broken, only Destruction remains". Celestia hears it, fearing for the lives of her former subjects and those of her beloved ponies. Unwilling to sit idle, she has chosen a dangerous path: return to the Imperium, take up the mantle of Emperor of Mankind, defeat the coming storm, and save Mankind once and for all.
With Twilight Sparkle to aid her, Celestia faces new challenges and new enemies. Her forces are scattered, her people assaulted, and the enemies of Man grow stronger with each passing day.
The Time of Heroes is gone. Now comes the Time of Ending.
Sequel to God Empress of Ponykind. Reading that first is strongly recommended.
Rated T for 40K related violence, but that might change at some point.
Comments contain spoilers. You have been warned.
This looks to be a great story! Lead them on Celestia!
FOR THE EMPRESS, FOR THE LION!
Remember my princess, Concordia Invicta.
Well this is going to be interesting, wonder how the Imperium will react when their Emperor returns as a xeno, and a female one at that.
You made a sequel!
And here I thought you were done with Pony-words! 
This makes me happy friend!
I haven't even read the first chapter (in progress) and I already know that is this going to be epic! You're awesome!
After reading: Soooooooo good. I can't wait to see what happens!
Maybe ... the Wolftime?
Sweet!
I wonder who the raven is?
Also, I can't help but wonder how effective the Emprah's last killing-off of the chaos gods was, given what they seem to have been involved with since.
6845162
Your Emperor returns! They're the same as they ever were, they're just a little horse.
Magnus is going to be involved! Yay!
Been looking forward to this.
Should I read the Luna fic before beginning this one?
6845427
Good one!
6845548 if you want to; most of the action here will be taking place in the Imperium, so what Luna's doing probably won't have that much of an impact
Chaos has granted us more emporer horse words!
Yay!
6846433
Is Celestia going to turn back into the Emperor? If Twilight comes with her, will she stay pony?
6846721 You'll see
6846784
If they stay ponies, I'll definitely follow this. The reaction of the Imperials when their Empress comes in would be rich!
6846904
Except you know Emperor used illusions to hide his true for more then 40k of years. So if he wish to become a man he will be. And let's face it humans will not follow a pony. Even less of a feamale pony.
On the other note I wonder what is Magnus up to. He is probably the only primarch in Chaos side who could return from this madness.
Oooh... A god of chaos warning the empress?
Now have you got in store for us iowa?
6847076 Fun*
* Iowaforever and the Four Gods of Chaos cannot vouch for any side effects of Fun. Please consult your local magos or medicae office if Fun causes any unexplained exhaustion or mutations.
6847086 *disbolically cheerful chanting in the distance*
Fun! Fun! Fun! Fun! Fun! Fun! Fun! Fun! Fun!
Fun! Fun for the fun god!
Hmmm, this is getting interesting...
6847086
Plus the Chaos Gods have different definitions of "Fun"
Hmm. Well, I guess there's only four beings who would summon their second greatest enemy to fight their greatest enemy (and of those four only two powerful enough to do it), and of those two one is dead, which leaves but one option.
Will be interesting to see where this goes.
I hope you Make them atleast Human now that they are in a Different Universe.
Because everything else would in the normal Warhammer lore just be a Huge clusterfuck which would end in the execution of Celestia and Twilight. Everything else would far to much go against the Known lore of the WH40k lore. the imperium is not a nice place and witchout atleast the Human card on their hand they wouldnt even get a chance from any higher up of the chain of command because they are Xeno and dogma says Xenos are liars.
Well , time to change the imperium for the better I guess ?
I mean , now Celestia can tell the Imperium how much they fucked up by herself (without needing a text to speech device , even) , so I guess that it would be a good time for that.
Celestia biggest allies in the Imperium would most likely be the Dark Angels... and outside of it she could maybe count on the Alpha Legion (If she was able to accept their help in the first place).
The Eldars... would be sneaky and crunchy like always.
And the Orks... WAAAAAAGH !
I think the biggest question here is, where's kitten at?
6847445
My money is on Eldrad, the galaxy's biggest dick.
You freakin' tease, you!
Well, I guess the Imperium is only getting one god to help them, rather than two.
6847729
that is were you are wrong my friend! For the Dark Eldar infamous leader Asdrubael Vect who is even a bigger dick than Eldrad shall ruin everyone's day!
Cleopatra was a Pharaoh, who is to say if the warrior strong enough should not be king? If not I'm not reading more.
6847551 WAFFLES! Waffles for the Waffle throne!
Heresy!
Oh this is WONDERFUL!
6847239 Smells like Dwarf Fortress.
Aha, so the REAL villain is....Games Workshop
Oke, I feel the need to adress not one but two huge elefants in the room.
First, now when the Emperor was sent to a different universe, Equestria as such didn't exist and the now turned she spent the better part of a billion years to create it right? While addmittedly time might run differently in every universe. If we say that only a couple of years passed since the Emperor left compared to the billion years on the other side, Celestias assumption of her and Twilight being away for a only a couple of months does not make much sense.
Second, and this one is a probably as big as the eye of terror. How can the Imperium still exist? I mean the Emperor was the pretty much maintaining the a giant holy space beacon that the Navigators used for guidance. With him gone the astronomicon should have vanished as well, making precision warp flights next to impossible. Wasn't that a factor in the downfall of the Earth Federation and the beginning of the Age of Strife?
I hope to see these adressed in a future chapter, but so far Im enjoying this greatly.
6847673 Probably at the imperial palace, staring at the now empty golden throne and sighing. I can see him being the first one to bearhug the Empress uppon return 'cause the alternative would mean he'd have to join his brothers in an abbs oiling contest. That and probably smacking the other High Lords in the head for trying to illegalize breathing, again....
6848299 To answer the first question, it's a matter of Celestia not knowing how long she's been away (hint: a lot longer than a few years) combined with a bit of underestimating how bad the problem is on the other side (either that or she's banking on the Warp acting weird again, but that sounds like a bit of a hand wave).
To answer the second question... Well if I did that I'd spoil a big chunk of the story
Hah this should be good. All hail
GodPonyEmperorEmpress of mankind!6848299
Read the Prequel
6848357
So can we expect Li'on/Guiliman/Russ/Vulcan/Magnus just yelling at his father for frolliking in another uniwerse when his people are suffering and being, well maybe not fine with this bot not thinking to hard a bout this. Funny when we think about it otehr Gods from Warhammer might to thinking quite low about Emperor now.
6848371 pretty sure he has. I didn't explain it there either
6847673
Needs more 4th-degree-inter-dimensional-warp-fuckery.
6847882
Well I know that, but I don't think he really has a horse in this race considering he cares for nothing outside of something threatening his rule over the Commorragh
(forgive the wording, it just came out)
I think deep down we all want If the Emperor has a text to speech device to be canon.
6848371
No no you are wrong. It's Man Emperor of Mankind.
And they're off!
Vulcan is going to be the Primarch who wants to pet his parent's soft fur when he sees her. (If he shows up.)
6847455
Oh Really?
The Big 'E' knows how to set people straight.
6847882
My bets on Cegorach.
MEN! WE NEED MORE ANGELIC CHOIRS FOR THIS!