Disclaimer: I do NOT own the Alien franchise. I would be the ultimate badass if I did.
Onboard a spaceship that belonged to the Engineers.....
The Queen was very displeased and has been ever since she was first put in her restraints. She wanted to be free and to thrive and after years of thinking, she formulated a plan.
In a pen, a lone Xenomorph rests in his restraints. He has large diamond-hard, razor-sharp blades connected to his hands. He also had ridges on his head, like a Warrior Xenomorph. However, he was a Ravager Xenomorph, physically stronger and had a tougher exoskeleton compared to his siblings. Since The Engineers kept many varieties of life forms for hosts on the ship. They were imprisand on the ship for experiments involving Xenomorphs. As a result, this particular Ravager was spawned from a Yaujta.
"Listen carefully my children" said the Queen.
The Queen and her subjects weren't physically able to speak. However they could communicate through a telepathic link. All Xenomorphs lessened in on the telepathic conversion.
"All Ravagers, I need you to bite on your inner jaws so you can use your acid blood to melt your bindings" said the Queen.
"We will do it mother" "yes mother" "finally, some action" said the Ravagers.
He got down to business and extended his inner jaw and bit down on it. Not hard enough to sever it off but enough to draw blood. The Ravager retracted his inner jaw for a moment to allow the acidic blood to pool in his mouth. He didn't need to worry about the blood dissolving him, it can't melt Xenomorph tissue.
Once enough blood had accumulated in the Ravagers' mouth he spat it on each wrist restraint. The blood melted through them in seconds. With his arms free he cut the restraints holding his bladed tail and ankles. He then proceeded to cut the door in front of him and the guards outside to peaces. This was why the Queen chose her Ravagers to start the escape. Their blades could cut through the tough composition of their cages and he could withstand a few blasts from their weapons. A loud noise then started blaring around him.
"They know you have escaped. Move quickly. Free your brothers" said the Queen. The Ravagers proceeded to slash the walls of the other pens, freeing more Xenomorphs.
"Thank you brother" each would telepathy say to him. Some nearby guards managed to hit the Ravagers but it only caused small chunks of armour to be torn away. The Ravagers themselves were OK so they and the other drones and warriors killed the guards quickly. They then went to free the others.
The ship was in chaos. Every Engineer on the ship knew that some Xenomorphs had escaped which meant they were in trouble. The security detail activated their laser rifles and ran as fast as they could to stop the Xenomorph outbreak.
A bladed tail suddenly appeared from a side vent and impailed one of the guards. They fired their weapons at the vent but the Xenomorph fled as quickly as it attacked. "There're in the ventilation system!" A guard yelled. He activated his wrist communicator "there're in the ventila-AGGGG" a Xenomorph pulled his head in to a ceiling vent. It then used its inner jaw to punch a hole into his skull, showering blood everywhere.
Elsewhere, five guards were looking for Xenomorphs in the engine room. Xenomorph movement was detected there. "Be careful where you fire your weapons. DON'T shoot any vital systems in here" the squad leader said. Putting extra emphasis on 'don't'.
HISSSS....
All the guards turned around and were jumped by a Xenomorph drone spawned from a Yaujta hunting hound. While it was stabbing one Engineer with its head horns it knocked the others over with its long, powerful tail. With one final stab it turned its attention to the others who were still a little winded from being pushed by the powerful tail. Said tail then stabbed one in the head. Then the Xenomorph jumped onto another, ripping his trachea out with its primary set of jaws causing another gush of blood.
Sensing that the three remaining had gotten up the Xenomorph scurried up the wall at lightning fast speeds. The Engineer guards tried shooting the Xenomorph but it dodged the laser blasts with ease. "Hold your fire, we don't want to damage---AGGGG" a human spawned Xenomorph warrior had sneaked up behind them. It had stabbed the middle guard with its bladed tail.
Using him as a body shield it grabbed the left guard and plunged its inner jaw into his skull. The Xenomorph warrior then flung the dead body off its tail at the last guard, knocking him over. It then jumped towards him screeching. The guard rolled out of the way and levelled his laser pistol. Only to be pushed onto his front by the hunting hound Xenomorph and accidentally shooting two laser blasts. The hunting hound Xenomorph stabbed him in the back of the head.
With their prey dead the two Xenomorphs scuttled out of the engine room. Completely oblivious to the fact that the two accidental laser blast disabled the engines.
The ship was dead in the water.
In Equestria.....
Twilight Sparkle, the newest Alicorn, had just announced to her friends about a big get together. It would involve all their friends and family.
"I'm sure my mother would love to come" said fluttershy.
"This is going to be the biggest, bestest, best party ever" yelled Pinkie Pie as she bounced on the spot.
"Oh that would be just splendid. All of us with our family members and friends" Rarity said with a dreamy sigh.
"The Apples are no strangers to big reunions so we'll definitely be there" Applejack said proudly.
"I'm totally going to introduce my family to the wonderbolts" said Rainbow Dash.
"Twilight!" Spike came running in "letter from Princess Cadence and Prince Shining Armour" he said. Twilight smiled "They must want to tell me who their bringing to the get together" she said. However, after unrolling the scroll her face fell and her friends took notice very quickly.
"What's wrong sugarcube?" Asked Applejack. After a moment of silence Twilight replied "they need us to come to the Crystal Empire. Something big fell from the sky" she said.
They were free at last and the Queen was pleased by this, she and all her children were out of their restraints. They immediately began to collect any hosts that were still alive and convert the crashed ship into a hive, they even found the outside of the ship. The Queen than remembered something 'How are your inner jaws' the Queen asked the Ravagers.
'It's doing ok, it has healed now' 'healed' 'still works' are a few of the phrases they replied with.
'Mother, there are suitable hosts approaching the hive' a Yaujta spawned Xenomorph drone said telepathically.
The Queen became excited "excellent, let them approach and when they get close capture them and prepare them for your new siblings" she commanded.
The Crystal Empire....
The mane six arrived in The Crystal Empire and they immediately saw what fell from the sky. A large c-shaped object that looked metallic, crashed a few miles away. The mane six noticed that every pony looked very nervous at this objects' presence, which was no surprise.
When they arrived at the castle the guards let them in and escorted them to the throne room. There they saw Princess Cadence and Prince Shining Armour. They walked up to each other "Hi Twilight, I'm happy to see you and your friends again" said Cadence.
"As are we, and I believe we saw what fell from the sky outside, right?" said Twilight.
"Yes you did, it happened an hour ago and I sent a detachment of Royal Guards to investigate, they should be back shortly" Shining Armour explained.
"None of us knows what it is but we are certain that the object is artificial" said Cadence.
"If those are aliens trying to invade Equestria we will stop them" Rainbow Dash boldly stated.
"No, if this object is alien in origin your job will to establish peaceful relations with them" said Cadence sternly.
"Honestly, must you always be so rash. I for one want to see their culture and sophistication" said Rarity.
"As soon as the detachment of Royal Guards return we will go" said Shining Armour.
With the detachment....
They came to inside the ship they were supposed to investigate. They also noticed that they couldn't move because they were cocooned in a sticky, slimy substance. Then there was the creatures around them, they were ghastly, disgusting, and scary above all else.
A corporal saw on some of his comrades faces a pail, bony creature with eight legs and a tail wrapped around their necks. When he looked down he saw fleshy eggs and the one that was in front of him opened at the top. He suddenly heard some pony yelling and turned just in time to see the pony's chest explode outwards. The corporal immediately panicked and tried to escape but another of those spider-like creatures jumped out of the egg in front of him.
Elsewhere in the Xenomorph hive...
An Engineer managed to muscle himself out of his cocoon. Luckily for him there were no Xenomorphs in the immediate area. He moved slowly and carefully to avoid detection fore he knew that Xenomorphs use sound as a form of tracking and navigation. He was also trying to find an atmospheric suit to hide his smell as that was also a way for Xenomorphs to detect him.
He found a laser rifle along the way and picked it up but he froze in fear when he heard a familiar hiss. He rolled out of the way just as the Xenomorph charged him. He levelled the rifle at the Xenomorph and shot it in the head. This made its acidic blood burst outwards in a small radius.
Knowing that the Xenomorphs heard the laser blast, he made a break for it. Running down the corridors of the ship, the lone Engineer shot several Xenomorphs before entering a room with atmospheric suits. He quickly sealed the entrance and got into one of the suits. He then opened the external door and with a wire cable, repelled down to the forest below.
The Crystal Empire....
"They should be back by now" said Shining Armour, worried. He, his wife, and the mane six had been waiting but the guards were overdue.
"Maybe they have been abducted by the aliens" speculated Rainbow.
"Or maybe they want something. I'd say we go investigate ourselves" said Shining Armour.
"Oh yeah. I'd like to see the look on their faces when we beat them" Rainbow said
Cadence turned to her husband "No, we don't know what we're dealing with. We---" she was interrupted by the sound of a baby giggling. She turned towards the source and found Flurry Heart peeking out from behind a door. "Flurry, now is not the time---" Cadence was interrupted again when Flurry flew past them out a window.
"No, she's heading in the direction of the crashed object!" Shining shouted as they all went after Flurry Heart. "Come with us!" Shining ordered some guards.
Later.....
The lone Engineer move slowly through the forest, scanning it all the while. He suddenly heard what he assumed to be vocalization.
"Flurry Heart, come out now!"
The language was different from his and he didn't understand it but he walked towards it. Xenomorphs couldn't talk after all which meant that a different, sentient organism was there. It could possibly help him and it was in danger. He put his scanner onto translator mode.
Elsewhere in the forest....
"Furry Heart, come out now!" commanded Cadence. In Flurry's mind, she was playing hide and seek with her family but she did not comprehend the possible danger. Suddenly, scary creatures with long, eyeless heads attacked. The fight was quick and swift, the creatures having the upper hoof in stealth.
Several ponies were taken alive back to somewhere but Twilight didn't know where. Rarity, Applejack, Fluttershy, and even Pinkie Pie were whisked away along with a few royal guards. Some of the guards were stabbed by the creatures bladed tails.
During the fight, Twilight saw Cadence get smacked by a creature's tail which caused her to be flung into a tree. This knocked Cadence unconscious.
"Cadence!" Twilight and Shining yelled.
Shining Armour tried ran to his wife's rescue but a segmented wrapped around his neck and pulled him into the foliage. Twilight flew up to avoid being attacked and to figure out a strategy. She observed the battlefield looking for a weakness in the alien creatures.
One unicorn guard that was pinned down by one of the creatures when he shot a magic blast at the creature's head. It died but the blood melted through his face, making him scream. Once the skin was burned away his skull was revealed before that to was melted.
"Acid blood! No fair" complained Rainbow Dash.
"How can we fight them if it's dangerous to us to hurt them?" Twilight questioned.
"We make them scared by showing them how awesome we are" replied Rainbow as she dived down.
"Rainbow, wait!" Twilight cried but rainbow was already gone.
Rainbow flew up to one of the creatures and punched it in the face. The creature simply looked back at her with its eyeless head, somehow looking angry. Rainbow laughed nervously before trying to make a quick escape but the creature's reflexes where faster.
The creature pinned Rainbow underneath it and opened its mouth, revealing a second set of jaws.
"Rainbow, NO!" Yelled Twilight as she landed. She then noticed three more of those long head creature with tubes on their backs. They were moving towards her.
Pang
Pang
Pang
The three Xenomorphs in front of twilight dropped dead, bleeding acid. Twilight then saw a tall, bipedal creature that looked much different than the hostile ones. It didn't have a long head and looked like it was carrying equipment of sorts.
It ran out of the bushes it was hiding behind and grabbed the creature on top of rainbow by its tail. Then, with amazing strength, the non-hostile alien pulled the violent creature off Rainbow and swung it into a tree. Twilight was impressed by the aliens performance, and the fact it was helping them. Due to this, she didn't notice the long head creature behind her.