Mechanos Chronicles: Take 2

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Ok I was really sort of unhappy with my lackluster performance on my previous stories. Part of it was that I wasn't really into it and also that it had a somewhat hokey feel. So I'm going to try again. The real title for this should actually be Mechanos Chronicles: Abridged Version since I'm planning on making one chapter with major plot and action sequences while the next chapter will give a summary of the major events in between the previous chapter and the next chapter.
Now I just need to work out some of my plot elements before I start. Seeing as its going to be different from the previous one by quite a bit, excpect this to take a while. I might also add that I might have some of your character's make cameos in the later parts.

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The Beginning

The Universe is a vast place. Within it are a seemingly unlimited number of galaxies composed of even more stars and planets. But even the Universe is not alone. Like the near infinity number of galaxies within it, there are a near infinite number of universes with each one being different from the other just as snow flakes. Many have a planet called Earth but not always is this Earth like ours.
Most of the time these universes will never know of the other's existance. But as there are an infinite number of universes they are constantly universes becoming connected and disconnected at seemingly random. These often go completely unnoticed never once affecting either universe. But sometimes something may cross these connections and cause major changes that can reverberate across both universes.
This is the story of such an event. It began in a universe extremely similar to ours. Infact the only real difference is that the earth is inhabited by two races of lizards instead of humans.
The first of these races are the Cilis. While they are small with their tallest members being only 3 feet tall, they are extremely intelligent and skilled at creating machines and tools that aide them in every day tasks. Despite this they have built a society that has little effect upon the environment they live in.
The second of these races are the Vong. Unlike the Cilis, they are large with the smallest members being 6 feet long while the largest can reach nearly 60 feet. As they have a more Hive like society with many castes that each serve a single purpose. They are nearly as intelligent as the Cilis but instead of relying upon machines of steel, the Vong breed hive members into the needed tool. Many of the resulting creatures are horrific creatures that have had armor and guns grafted directly into their bodies. Also the Vong tend to create colonies that are unsustainable. They will use the local plantlife to feed their primitive foundries while their hunter castes will drive all animal life to extinction within the area. When they have completely spent the local resources they will pack up their entire colony and move on to the nearest unspoiled area.
Needless to say the differences between these two races have resulted in many wars with the machines of the Cilis battling against the beasts of the Vong. After thousands of years of constant warfare the Cilis were finally able to drive the Vong off of their planet and into the cold reaches of space.
After a few centuries of peace and the colonization of several nearby planets, the Cilis had nearly forgotten about the Vong with the only reference being to scare naughty children.
But the Vong were not finished. All but one of their colony ships died leaving their inhabitants to die a slow death. But the last one finally reached a habitable planet. Then they began to rebuild for their conquest.
They would soon be ready to avenge their loss and reclaim their home planet.

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First Contact

For centuries the Cilis had been at peace as the slowly moved out into space colonizing uninhabited planets as they went. When they came upon other civilizations they would attempt to start diplomatic relations and open trade routes. Those that accepted found the Cilis to be extremely helpful often improving their societies immensely. Those that rejected these offers and turned hostile against the Cilis found them to be benevolent enemies. The Cilis would depart the planet leaving a small satelite at the edge of the system to act as a calling card if the civilization should ever change its mind. They also didn't stop trade between the system and other systems but would immediately halt any warships that attempted to enter Cilis space.
In the end these efforts paid off greatly for the Cilis. Those planets that had accepted from the beginning eventually entered into the Cilian confederation and those that had declined would almost invariably open trade with the Cilis after becoming enthralled by the Cilian goods they would recieve through second-hand trades at steep prices. Eventually even these xenophobic societies would join the confederation.
Thus the Cilis' influence spread all across the galaxy. Even in areas where no Cilis had ever set foot they would likely be greeted warmly. The Cilis were even known of in several of the nearby galaxies thanks to wormhole technology. It seemed that eventually the Cilis would unite the entire Galaxy under their confederation.
But this changed when a Cilian scout cruiser came out of a wormhole into a previously unexplored system. It was a fairly harsh system with a young star that spouted jets of plasma far into the solar system. A quick scan revealed that almost all of the planets were dead husks bathed in radiation. But the last planet, which had an orbit that was about where Neptune's would be, showed some signs of sentient life. As the ship came closer they could seem massive structures from space that looked natural but looked oddly like artificial stuctures. As the cruiser came closer they could could make out trails of smoke coming from towers on the formations. As they finally landed they prepared for what they presumed would be a primitive insect society. They loaded thier vehichles with simple devices that would make farming of fungus and plants easier along with trinkets that insects seemed to find enthralling.
As the ramp came down and the Cilian transport came down the ramp they were suprised by the smell of the atmosphere. There was a musky smell that for some reason caused them to feel nervous. None of them had ever smelt it before yet it seemed familiar. After taking a few minutes to calm down the scouts headed in the direction of the nearest structure. As they went they had the odd feeling they were being watched despite the fact that ever since arriving upon the planet they hadn't seen any animals. The entire scouting party kept their hands close to their weapons. They could tell that something wasn't right with this planet and they weren't about to be caught off guard.
As they finally came to the structure they found a large entrance that had a heavily worn path in front of it. Engraved across the door were strange pictures that made the Cilians even more uncomfortable. Many of the images depicted Saurians much like them but these seemed bulkier and almost all of them were in the process of killing and eating smaller Saurians that looked exactly like Cilis. They were about to cut and run when the door began to open.
The Cilian stood their ground as the door swung inward revealing a single Saurian. It was nearly double their height and was far more bulky but it also seemed to be an aged creature with wrinkles acrossed its dull red scaled skin. It held a cane in its right hand and appeared to be unarmed. The Cilians calmed down upon seeing the first thing that made sense. Now they just had to get their translators ajusted to the local language.
But when the Saurian spoke they were amazed that their translators already seemed to have the language in its memory banks.
"We greet you, star lizards. Our prophets have forseen your arrival since the beginning of our Exile. With your arrival our gods shall grant us our home world again."
The Cilians were unphased by the prediction of there arrival. Almost every society had prophecies of the arrival of some saviour that would deliver them from oppression, help them crush their enemies, or other such things. Even the Cilis had such a legend that a being would arrive to save all existance from doom. The Cilians decided to play it safe by neither confirming nor denying they were the ones foreseen.
"We have come from a distant star bearing gifts and an offer of friendship and cooperation between our people."
"This too was forseen and we shall follow what our prophets have instructed us to do."
The Cilians suddenly noticed that several Saurians had emerged from the undergrowth behind them and more were arriving every second. When they turned back to the elder Saurian they found him flanked by two massive Saurians that seemed to be an entirely different species. The Cilians were now a bit unnerved but were sure they could find a way out.
"Sir if your people do not wish to accept our offer we will kindly leave and bother you no longer."
"You have not bothered the Vong. You have fufilled the first part of our prophecy."
Upon hearing the word Vong all of the Cilians eyes bugged out. They had all been told in their childhood that if they didn't behave the Vong would come and eat them up. The Vong had been presumed to be extinct for centuries.
One of the more forward thinking Cilians managed to quickly send the recording of the last few minutes to the scout cruiser and kept the link open.

On the bridge of the cruiser the crew recieved the message and the feed. While the crew listen to the feed one of the comm officers listened to the recording.
"Your arrival has heralded the beginning of the Great Conquest. You shall serve as the first sacrifice to thank our gods for letting us live to take part in the cleansing of the galaxy of your pathetic race."
The last few seconds of the feed consisted of roars, squeals, and the sound of breaking bones before there was only static.
Just as the feed was cut off the comm officer jumped out of his seat screaming, "THE VONG!!! IT'S THE VONG!!!"
The rest of the crew bugged out as the captain tried to regain control. He was finding it difficult until a blast caused the ship to shudder. As they looked out the bridge window they could see several large creatures marching towards the ship. The creatures held there tails over their backs which seemed to have a barrel sticking out the end of it. This was confirmed as one of the beasts fired with their tail causing the ship to shudder again.
"Men we've got to get out of here quick! Somebodies got to get out a warning fast!"
The crew immediately knew what they needed to do. They got to their stations and skipped almost every safety procedure in the book in the desperate attempt to take off. As they sped off into space several Vong warriors clung onto the craft with a death grip that only became tighter as the craft entered the cold vacuum of space. As the craft made a dash for the nearest clear warp point several Vong craft followed in hot pursuit. As the Vong looked back they realized the craft were infact animals just like the tanks had been.
As the craft finally closed in and were about to latch onto the cruiser, the Cilians made the jump into hyperspace. One of the Vong craft was sucked into the wake but due to not being bred for hyperspace travel it died almost instantly

In a nearby system a cruiser came out of hyperspace. Behind it came another craft that drifted behind the cruiser. On the nearby planet a comm hub operator addressed the cruiser.
"Scout Cruiser Good Hope, we didn't expect you back so early. I presume you didn't find any--"
"The Vong! They're alive! You've got to warn the entire confederation!"
The operator rolled his eyes. Another crew that must have hit a hyperspace distortion. Usually drove the entire crew mad as they had the entire history of the universe pumped into their head in an instant.
"Good Hope we're going to send a Med team. If there are any still sane members of the crew on board then please put on your gas masks."
"We aren't crazy! We've seen the Vong!"
"Yes sir I'm sure you did but we're going to have to follow procedure."
"Wait! We've got some proof! Petty Officer get a camera and point it at that corpse on the hull. You've got a video screen on that end right?"
"Yes sir but I still think you're not in your--"
"Shut up and turn it on now!"
The operator rolled his eyes again as he turned the monitor on. At first he didn't know what he was looking at. It was shaped like a reptilian face but it was somewhat fuzzy.
"Could you fix the focus please."
"You heard the man!"
As the image came into focus the operators jaw slowly dropped. It was the face of a Saurian but it was extremely scarred and seemed to have metal plates grafted into it. His jaw finally went fully slack as one of the Crew members stepped infront of the face. The face was nearly as large as the Cilian!
"And there's something else you should see."
The camera panned over to the right. A craft came into view that looked like a heavy fighter. But as the operator looked at it more he realized it was a Saurian much like the other but its body was extremely distorted and covered in metal plating, weapons, and engines.
"P-p-please h-h-hold."
The operator pressed several butons with shaky hands.
"H-h-hello. I-I-I need to sp-sp-speak with the Confed Defense C-c-command. This is a l-l-level 5 priority and I've j-j-just sent the verification codes. The Vong are alive."

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War Effort

Within days the Cilis were converting factories into weapons manufacturers. Due to the centuries of peace the only weapons the Cilis had were meant more for light combat and not the heavy combat that was predicted to come. Thus the Cilis were forced to search through their ancient records for the weapons their forefathers had used against the Vong.
Soon the Cilis possessed a sizable fleet of large, though antiquated, warships. Battle groups regularly arrived at border colonies along with large shipments of space and surface weapons.
2 months after the first contact the first attack came. On the edge of one of the more recently colonized systems a single Vong cruiser came out of hyperspace. It was a twisted looking creature with much of its body being covered in metal plating. Poking from between the armor were the large crystaline eyes of the beast. It lacked an external mouth as it kept its food and air in large internal organs. Dotting its surface were many turrets that were either metal weapons such as mass drivers and lasers or more insidious biological weapons that were esssentially smaller Vong that had been grafted into the ship's skin. Many of these shot biological slugs that could eat through star ship hulls and then release toxins once inside the ship. But alng the sides were a line of such bio weapons that were meant specifically for short range attacks. They launched grapling hook like tenacles that would burrow through the side of the ship. Once inside they would serve as a means of boarding the other ship.
Despite it only being one ship, the Cilis could tell it was a lethal threat even by itself. They moved to engage the ship but tried to stay at their weapons maximum range. The Vong cruiser put up a fierce fight but eventually was destroyed. As the Cilis celebrated their first victory some realized it may be their last. They had lost twelve ships in an effort to destroy only a single cruiser. It had only been a scout probing the defenses and it had found them to be lacking.
Thus the Cilis engineers began to design counters for the weapons that had been encounterd on the Vong ship. They also began to design better land weapons for the inevitable surface battles to come.
Thus began the Mechanos Project.