The Uneasy Alliance

The Uneasy Alliance

by AJ Marks

Part 1

The saucer shaped ship scanned the planets of the system it was assigned to patrol, on the lookout for the renegade battlestar, Galactica, and the fleet of humans it protected. For too long the last remnants of the human race had eluded them, a plague which refused to go away.

Approaching the third planet in the system the Cylon crew went about their duties but were suddenly perplexed by something new. The planet’s atmosphere of dense electrical storms disrupted any possibility of the scanners penetrating the planet to see what was going on on the surface of the planet.

A decision was made by the commander of the basestar and a patrol was sent out.

The Cylon raider easily penetrated down through the atmosphere but what it sent back astonished the basestar commander, something he had not expected to encounter, or at this level. He quickly sent a report back to the empire and waited for a reply.


A large city, unlike any ever built by humanity surrounded by a huge harvesting field and power supply. Unlike the past where the city was used by humans, this one was used by humanities children and humans were used as the power supply.

Machines were working to try and undo the damage done to the sky so long ago. The intense electrical field would damage them if they went too high, but if they could disperse the clouds then they could get their energy from the sun again allowing for real healing between the two sides.

The machines and humans had already agreed that those in the Matrix would stay for now and remain in the dark. It would be chaos if everyone suddenly knew what was going on.

An alert suddenly sounded as three saucer shaped ships appeared, unlike anything anyone had ever seen before. What surprised them was the fact these ships opened fire upon the harvesting fields and where the humans were housed.

The attackers were accurate destroying thousands of humans before the defenses rushed to counter the problem. In seconds it was over but confused everyone, who attacked and why?


A man looked out over an area where several children were playing, their voices reaching up so he could hear their laughter. It was something he never thought he’d hear again as the war had been too close this time, even closer than anyone would know.

He looked up having a strange feeling, it wasn’t much but he understood something had happened only he could not completely figure it out. He only knew it had to do with the Matrix itself, and perhaps beyond.

The war between the people of Zion, the last free humans, and the machines ended almost a year ago changing everyone’s lives. Yet he couldn’t shake the feeling something was wrong.  No one had heard from the machines since the end of the war, and going into the Matrix was considered a violation of the treaty.

The machines had kept their agreement, anyone who found out about the Matrix left, handed over to the people of Zion. So far only thirty people had come and most adapted better than anyone hoped they would.

He turned sensing someone coming towards him and looked to see his wife heading his direction. Their relationship had blossomed after the last battle and realized somethings were worth reaching for asked her to marry him.  Now he was glad he had taken that step.

“Morning gorgeous,” he said as she reached him, giving her a welcoming kiss.

“That was nice, but what’s wrong, you know I can tell, you’re tense,” she said to him, as he realized he could never keep such things from her.

“What makes you think something is wrong?” he asked, trying for a look of innocence as he normally did when she asked such questions.

“Because Morpheus, I can read you like a book,” she replied glancing directly into his eyes.

“Look around, kids are laughing and playing, we’ve been at peace for over a year now, our population is finally beginning to grow again after that last battle, what could possibly be wrong?” he replied to her question looking back down where the children were playing and having fun.

“Because I can feel it,” she said reaching an arm around his waist. “You’re twitchy and nervous about something, I haven’t seen it this bad since Neo and Trinity left to the Machine city, now what’s going on?”

“I can’t explain it, it’s only a feeling that something is going on and is very wrong,” Morpheus replied to her unable to fully explain it.

“Then why don’t we go and find out,” Niobe replied plainly causing him to look down at her wondering if she was stating what he thought she was. She appeared to be as anxious to figure out what was going on as he was.

“And how do you suppose we do that? It’s not like we can just hop on over into the Matrix, that’s forbidden,” Morpheus said to her.

“I know, but once inside we make contact with one of the agents,” Niobe said.

Morpheus thought about it for a few seconds. Announcing themselves right away might help, or hurt.  He had no idea what type of reaction the agents would give him.

“It’s risky,” he finally stated.

“Of course, the Hammer’s systems are still operational, and I bet Link would be willing to help us,” Niobe said giving Morpheus something to think about.

“It goes against the Council and treaty,” Morpheus said but it was only a half argument, he wanted to do it from the moment she mentioned it.

“Yeah, but when do you adhere to the rules?” she asked, as a grin formed on his face.

“Let’s find Link,” he said, turning to walk away from the children.


Deux Ex Machina pondered the fact it learned from the recent attack upon them. The ships had been examined and determined to not be human and the logical intelligence indicated the attack came from above the clouds, somewhere either above the clouds or from outer space.  The defenses quickly overwhelmed the ships but the firepower of the ships was immense and superior to anything they had.

The facts disturbed the big machine a lot. It thought about where the attackers came from.  It could be some sort of floating city whose history had been lost.  But that thought brought up another question, were they human or robot controlled?  Were they even from Earth, or from somewhere beyond and if so why did they attack?

The attackers also quickly figured out where to attack them where they were most venerable, the humans providing power to their city. So they either knew a lot about such things, or had been studying them for a while.

Going over the facts of the war against the humans they had never attacked the fields. It was almost an unwritten rule by both sides, considering the humans were fighting for freedom from the Matrix it made no sense to kill their own.  So it came to the conclusion they were probably fighting a new threat, one it must quickly understand before it was destroyed.

Of course it also became clear there were several immense problems for the machines. The threat came from above the storms, the intense electrical currents still raged and rendered all controlling robotics useless, meaning the Sententials were unable to go above the clouds to see what was going on.

He suddenly recalled a memory from a recent battle when the human named Neo had entered the city. His craft had briefly flown above the clouds and returned still functioning.  Perhaps they could use that to help them.

It was an interesting fact to think about, especially considering the fate of the machines might be in doubt, would the humans help them? The irony of the situation was not lost on Deux Ex.  The only question became how to contact the humans.


Two black centurions approached the Imperious Leader, leader of the entire Cylon Empire, who sat on his raised chair in the middle of the room. It had a large metallic silver sphere of a head with no discernible features and looked like a mass of wire.  The two black centurions represented the next generation of Cylon warriors, keeping the same body type, but black improved armor and more maneuverable than the previous series.

“Speak centurions,” the Imperious Leader stated, waiting to hear the latest reports on the Empire and what patrols might have encountered.

“By your command,” the centurions said in unison before one continued. “A basestar has reported finding a planet full of humans.”

“Humans?” the Imperious Leader said now interested in the report. There had been no reports of humans since the end of the war with the Colonials, and yet the humans still plagued them with the fleeing remnants including the last battlestar, Galactica.  “Where?”

“One of our far patrol basestars. Preliminary reports by the scouts indicate billions of humans, but there was also something strange with this group that confused the basestar commander,” the centurion reported giving the Imperious Leader terrible news.

“Strange, how?”

“The humans are encased in tubes in large towers, and the scouts reported they were under attack by unknown ships, after which the basestar lost contact, they are presumed to have been destroyed,” the Cylon explained.

“Tell the basestar commander to attack at once, find out the full abilities of the humans,” the Imperious Leader ordered, concerned with the number of humans.

“By your command,” the centurions replied turning to carry out their orders.

The Imperious Leader pondered the recent sighting. Still no contact with the Galactica, but this many humans was concerning, especially if they could fight the Cylon Empire.  He did not want another war with humanity, they had to be destroyed once and for all.


Morpheus and Niobe quickly made their way towards where Link now lived hoping that he was hope and they would not have to talk with his wife. They both doubted she would be as understanding with what they wanted to do.

Knocking both waited anxiously before the door opened revealing Link much to their relief.

“Can we come in?” Morpheus asked.

“Yeah, sure, it’s great to see you both,” Link said, inviting them both in.

Morpheus looked around seeing no one inside while sharing a glance with Niobe before turning towards Link, who had cut his hair as a result of a toddler.

“Its been far too long between visits,” Morpheus stated sitting down at the table as Link brought over some glasses of water before sitting down as well and looking at them.

“So, what’s going on?” he asked.

“Going on?” Nioble asked.

“Yeah, you don’t work for Morpheus without knowing his faces, he’s thinking about something, so what is it?” Link asked being direct.

Morpheus gave it some thought, now that they were here it seemed much harder to ask especially considering Link had not done anything yet.

“Before we say anything, I want you to know that you don’t have to do anything, or even come with us,” Morpheus finally said to him.

“All right, now I’m really curious,” Link replied.

“We want to go back into the Matrix,” Morpheus stated plainly not surprised at the look Link gave them, both knowing it was against the treaty. “I don’t have a good reason, only that there is a feeling that something is going on, I don’t know what, but we need to find out.  What do you say?”

“Let’s go,” Link replied before Morpheus could say anything else surprising him while grinning. “Haven’t done anything exciting in a while now.”

The three of them left heading towards one of the remaining ships in the fleet, the Hammer, but they also had to avoid guards who would ask too many questions even of heroes of the war. Morpheus was in hurry, the last thing he wanted to happen was to be detected.

Finally after an hour they managed to get inside quickly heading to the back where the equipment was. They could get into the Matrix from here, during the war hey didn’t due to fear of tracing.  Now they hoped to be in and out before anyone here noticed.

Link went over quickly booting up the equipment as Morpheus went over and sat down, looking over at Niobe as she did the same.

“What are you doing?” he asked.

“Going with you, you might need backup and I’m it,” she stated calmly sitting in the chair as well.

He thought about arguing but knew It would be useless and shared a look with Link, who had finished booting up the systems. Giving him a thumbs up Morpheus relaxed a bit feeling the interface link up.

Next stop, the Matrix.

End part 1

Continued in part 2

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