This AU takes place in the first year of the Human-Covenant war, and around 50 years before ME 1. Probably a one-shot.
UNSC Outer Colony world of Avalon
Governor Constantine was pacing around in his Panic room. Some aliens, who were not the Covenant, were attacking his colony. Last he heard the orbital defense fleet destroyed nearly half of the Attacking forces before retreating. His military advisor estimated reinforcements to arrive in around, at least, or under twenty four hours. Ever since the 'Covenant' Glassed Harvest, Arcadia, Shanix and so on, The UNSC has been looking forwards to destroying some more Covenant warships and raise moral.
So it's only logical for them to arrive and destroy the attacking aliens. In the Panic room also sat General Hal, he was commanding the troops from the emergency command center in the Governors panic room, ever since the aliens bombarded his actual command center he had to use this one, the General himself was a rather young general, yet very experienced. From what Constantine knew he served as platoon commander during an uprising not to long ago and during that failed uprising he was promoted to General.
As Constantine looked on to the holographic display of the only largely populated city on the planet, he saw how quite a lot of Red Dots where converging on to the Green Dots, which were the UNSC forces, the Governor then nervously asked
"What's are situation?"
"Well, we are screwed that's for sure."
"Heh, well it better than being Glassed."
"I don't know, these aliens" Hal said as Holographic displays of an Avian like spices, a Human-Like spices just in-Blue and a turtle like species appeared "Could treat prisoners like food"
"Well I most certainly don't hope for that to happen. Just bec-" the Governor was cut short as gun shots could be heard from the other side of the metal door
"Shit! They are fast! Marines move it!" ordered Hal
With their orders technically given they took the Governor and headed to the secret underground tunnel system. General Hal sighed as he heard the blast door being blown open and the sounds of gun fire. He didn't even look back, he just took out two magnums and turned to see the fire fight between his troops and Blue Chick aliens and the Brid heads.
Avalon, 53rd street, Avalon city
Lieutenant Sorman of the Turian Hierarchy looked at a fortified Anti Air machine gun emplacement and its eight occupants. These primitive creatures were around his own height, and looked a lot like Assari, just fur on top of their heads, with different colors, and With Males, the Hierarchy was going to subjugate them very easily, they still used chemically propelled weapons and didn't even use Element zero, although their guarding fleet of four Cruisers tore the Citadels fleet apart, they were quickly destroyed as were their in-system mining stations.
Nevertheless, he and his company was in charge of destroying that emplacement. And so he would do. But just as he was going to open fire, he saw the leader of the Natives raise his hand, and then instantly the others under its command tensed up and looked around.
He could hear them say "Sargent jack here" the creature then moved its hand to the left side of its head and then listened closely it then said "Shit! Move it up! We got Covenant Banshees on an incoming attack run!" it then moved its hand in a swivel in the air and the AA gun moved to face the sky. Suddenly he could see some strange incoming fighters. He checked in and found out his Comms was being Jammed. All of the Creatures immediately started firing at them downing three before the purple colored fighters engaged and destroyed the AA encampment.
Once the Encampment was down he looked at his Omni tool and read a report from another company stating that they are seeing the massacring of the Primitives, Civilians and Military, by some unknown aliens.
CSS Glorious Pacification, Avalon system, preparing to glass the colony
Shipmaster Tek' Valdur looked out of the window and saw the pathetic Human colony and the Unknown aliens attacking it. At least even theses aliens know when to attack the enemies of the Forerunners. The destruction of Pathetic Human orbital defenses and their space station was going to make it so much easier for him to glass the planet. Of course, his Sangheili Spec Ops warriors were itching to get a fight, so he sent them down to toy with the Humans a bit before he glassed the Planet.
The Aliens hailed him multiple of times no doubt wanting him to go away so that they could claim the spoils of their raid. However he would ignore them and Glass this planet as the Holy Forerunners demand. Nothing shall remain.
-67 minutes later-
All of his warriors had re-entered the CSS class Cruiser and he shall momentarily begin glassing the planet. Just as he began thinking rationally. He remembered that the Aliens know nothing of the Covenant, and how they remove the Human Vermin. He must remove them. So he told his communications officer to un pack the first contact package and hail the ships.
He was greeted by a very Chaklak(Bird)-Like alien who betrayed no emotions the alien then said "Greetings I am rear-Admiral Valaras of the Turian Hierarchy representing the Citadel council. How are you, if I may?"
"I am Shipmaster Tek' Valdur, of the Holy Covenant Empire. On behalf of the Prophets we thank you for destroying the Vermin's pathetic defenses. But please call your troops back so we may start glassing operations"
"Glassing operations?"
"Yes, we shall cleanse this planet with our glorious fire until the Planet is only but a dead rock, free of this Human filth"
"Excuse me what?!"
"You sound surprised. Do you not exterminate these Aliens as the Forerunners Demand?"
"What?! No we don't exter-"
"Then you shall die with the humans"
Tek' said as the channel closed and his ship opened fire, almost instantly destroying the alien fleet. Their colonies will be found and exterminated, and their home world subjugated. But for now he will Glass the planet.
And that's that. Please feel free to continue the Human-Covenant war with Council interference.