The Uneasy Alliance – Part 2

The Uneasy Alliance

by AJ Marks

Part 2

Morpheus closed his eyes then opened them back up looking around at a familiar sight once more and realized despite everything the Matrix hadn’t changed at all. He looked over as Niobe joined him and they headed off down the street, Morpheus heading towards the building where the agents held him almost a year ago when Trinty and Neo had rescued him.

He passed by several people, everyone seemed content despite the fact he knew everything around them was faked. A couple passed him as he continued walking a bit nervous about what to expect by any agents.

“Morpheus,” a voice said causing him to turn around to see to men dressed in black suits, agents. He paused a second noticing they were not heading to attack him, or anything else.

“Yes,” he finally replied, stealing a glance over at Niobe who waited as well.

“We’ve been expecting you, follow us,” the other agent said, turning to walk away assuming they would follow.

Morpheus shrugged at Niobe but followed anyways. He felt confused at the reaction, how had they been expecting him, and why?

“You were expecting us? Who told you?  And where are we going?” Morpheus asked his curiosity getting the better of him.

“To see the Oracle of course,” another voice said from behind him causing him to turn to see a man with black hair, Asian looks standing there. “Hello Morpheus, you know this is a violation of the treaty,” he said to him.

“Seraph,” Morpheus said, giving him a slight bow before realizing what he said. “The Oracle knew I was coming?”

“Of course,” Seraph replied. “If you wish a more detailed answer you must ask her.”

Morpheus gave some thought to that and had no idea how the Oracle would know this. He understood she was a computer program of the Matrix, but still seemed wise beyond any of the other programs.  They reached her apartment and walked in, everything seemed as normal, the only thing missing was the number of people this time.

“She’s expecting you, go on in,” Seraph said placing a hand on Niobe’s shoulder indicating Morpheus should go on alone.

He walked into the kitchen seeing her, she had changed a bit but the kitchen appeared normal.

“Hello Morpheus,” she said in a warm voice. “Cookie?” she said holding out the tray to him showing a grandmother-like quality she always had no matter what form she took.  He took one and ate it despite knowing it wasn’t real.  “How does this batch taste?”

“Excellent as always,” he replied.

“Sweet talker, but it’s nice to know I haven’t lost my touch,” she replied putting the tray down and sitting down to face him. “You probably want to know how I knew you were coming, and what is going on.”

“Yes,” Morpheus replied a bit shocked she has seen through him so easily.

“I am part of you, like you are part of me. When something is wrong with one the other feels it, we have much to talk about,” she told him.

He sat down waiting to hear what she had to say.


Deus Ex hovered keeping an eye on the Matrix and what was going on in there. He had been informed the moment humans from Zion had been spotted and hoped the information would be relayed with help.  It also kept an close eye on the sky anticipating another attack.

Suddenly a formation of ships broke through the clouds streaking towards the human fields and energy towers. Almost immediately defense forces rushed to greet the attackers who opened fire once more without warning.

The Sentinels quickly ripped apart the attacking ships but there was mixed results. While the ships were ripped apart, they were tougher than expected and several shots landed in the fields, whoever the attackers were they were good shots and relentless in their attack.

With more ships the damage sustained was larger this time and with several well placed hits the fields lost several thousand humans connected to the Matrix which would have to be rebooted again.

Deux Ex hoped the Oracle could convince the humans to help them out in this new struggle. If they didn’t find out who was attacking them, and from where they might be destroyed.


Morpheus looked over at the Oracle wondering what they would have to talk about, the peace between the Machines and Zion appeared to be benefitting everyone at the moment, and both sides were getting along, or so he thought. Had someone done something?  He then noticed a strange look on her face as she listened to something far away he couldn’t hear before looking back at him with sadness in her eyes.

Before he could even ask what was going on everything wavered for a second then went completely black followed by a blinding white light. He almost freaked out before seeing everything being rebuilt in just a few seconds and he found himself standing back in the Oracle’s kitchen with her standing there.

“What was that?” Morpheus asked unsure what had happened when his phone rang. “Hello.”

“Morpheus, what the hell just happened?” Link’s voice said, a touch panicky. “All my screens went haywire.”

“I don’t know, but I’ll find out, I’ll keep in touch,” Morpheus said turning to the Oracle who appeared to be waiting for him to end his conversation.

“What you saw was a full reset of the Matrix, I’m sorry I didn’t have time to warn you before it happened,” she said to him still not saying why the Matrix had to be reset. Was there a problem with the program?  “We are fighting a new war Morpheus, one which it seems we need your help to survive.”


Two vipers streaked through the vacuum of space on a simple patrol to keep an eye out for any signs of Cylons, life or supplies they might be able to use. So far the patrol had not found anything worth taking back to the Galactica, nor had they found much of anything lately.  They had passed a few planets which had been rich in tylium helping the fleet replenish their fuel supply.

“Hey Starbuck, you see anything on your scanners?” Apollo asked while they were searching another solar system, it had a few planets, some might be considered interesting prospects.

“Don’t think so,” Starbuck replied.

The patrol had been boring so far and in a way its how Apollo wanted it to stay. However a part of him wanted something, anything, to happen.  He wished to find something which might help the fleet in the journey.

“This system appears barren, wait, hold on,” Apollo said looking at his scanner. The system had been uninteresting by now he had an anomaly on his scanner.  He waited a second allowing the computer to analyze it before returning the results and his blood ran cold.  “Starbuck, hide now,” Apollo said turning his viper into the nearest planet’s atmosphere.

A quick glance at his scanner indicated Starbuck had also headed to the nearest planet while they both waited a second.

“Starbuck, you still there?” Apollo asked a few microns later.

“Yeah, but what’s going on?’ Starbuck asked despite the fact Apollo was glad to hear his voice.

“My scanner picked up a Cylon basestar,” Apollo replied. He turned his viper back up out of the atmosphere and scanned in the direction of the basestar relieved a bit to not see it.  “I don’t see it anymore, let’s get back to the fleet.”

Starbuck didn’t argue as they both left the system as fast as the vipers could travel headed back to the fleet keeping an eye out for any patrols. The last thing they needed was a Cylon patrol finding the fleet now.


Morpheus sat down a bit stunned by what the Oracle told him, and confused as well. If what she said was correct then a new type of machine had shown up and attacked the Machine City along with the humans providing power to the city.

Looking over at the oracle, who calmly waited for a reply. He considered her request to be genuine and he never knew her to lie to him so why would she start now?

“Who are you fighting?’ Morpheus asked despite already knowing the answer but wanted time to think about his answer.

“We’re investigating the wreckage, but whoever they are we’ve discovered no human bodies,” the Oracle replied. “From reports I’ve been given the pilots are some sort of machines, but we have no idea who controls them.”

“Machines,” Morpheus said unsure if he liked the idea of going back to war against some sort of machine race, or a group which was a spinoff of the group they just made peace with. “What type of machines?”

“Honestly Morpheus, we don’t know,” the Oracle replied back to him. “All we know is they appeared from above the clouds and attacked us.”

“Some sort of left over machine from before the sky was torched?” Morpheus asked, he needed as much information as possible, especially if the machines were asking for help against them and he had to go to the council. No one knew much history beyond what they learned in the Matrix, and that wasn’t known how true that was.

“We have no such files of any machines leaving Earth,” the Oracle replied.

“Then they are a mystery. So what do you require from us?” Morpheus asked getting down to the heart of the matter now.

“We have a plan, but we need your help to pull it off,” the Oracle said, then began to outline the plan to discover who they were fighting and how to get above the clouds.


Apollo and Starbuck made their way towards the bridge of the Galactica both knowing how hard it would be to inform the commander of what they encountered during their patrol. The last time they encountered a Cylon basestar Commander Adama decided to attack rather than try to go around, a bold plan devised which could have been disastrous.  Apollo had no idea how his father would react this time.

They both had scanned the system for any other signs of nearby basestars to see if this was a lone ship or not and the lack of anything worried Apollo. He figured his father would increase the numbers of patrols which would only strain the fuel reserves of the fleet, but also knew the fleet didn’t have the reserves to fight a prolonged war against the Cylons.  He hoped they had a choice.

He went over everything about the encounter and the only thing which seemed strange to him, what happened to the basestar and where did it go. He didn’t see it again even after they left.  It was a long time to be behind a planet considering the orbiting speed of a basestar.

Making their way onto the bridge he made his way to the commander with Starbuck following right behind him. The bridge was its usual hub of activity as people went about their jobs to make sure the battlestar continued to function as best as possible.  The warships systems usually functioned better than other ships as they were designed to take damage and be redundant.

Apollo noticed his father and headed over towards him, watching as Colonel Tigh came over as well to hear the report.

“Apollo, you told Tigh you found something?” Adama asked as Apollo reached him. Apollo noticed that his father hoped for good news, not the news he had about a Cylon basestar.

“Um, yeah, but its not good,” Apollo said seeing that he dashed his father’s hoped of some good news for a change. “We ran into a Cylon basestar while scanning the system.”

“Are you sure?” Tigh asked, his tone indicating he hoped Apollo and Starbuck made a mistake.

“No, but I don’t think we were detected, we hid rather quickly,” Apollo said knowing that if they had been detected the Cylons would already be at the fleet by now.

“So you weren’t spotted, how?’ Adama asked.

“We ducked into the atmosphere of the local planets to hide,” Starbuck said.

“When we came back out the basestar was gone,” Apollo stated. “I don’t’ know where it went as we never spotted it even after leaving the system.”

“They could be setting another trap for us,” Adama finally said quietly looking over at Tigh.

“Possible, if so what do we do?” Tigh asked.

“If so we need to find out when and where, if possible, I don’t want to walk into another trap,” Starbuck said to them.

“There is one other thing, now that I think about it,” Apollo said, having gone over and over the encounter. “It seemed like that basestar was going fast, for it to go through the system in the amount of time we were in the atmosphere, it doesn’t make sense.”

“It goes against their operational procedures as well,” Adama said, sitting down to think about the situation.

“You think that’s why they didn’t spot us, they were in a hurry to be somewhere else?” Starbuck asked.

“It’s the only thing which makes sense,” Adama said before looking up at Tigh. “Increase the patrols briefly in the direction of the basestar, any other nearby systems as well, and let’s keep it quiet for a bit, no need to start an unnecessary panic among the people of the fleet.”

“On it commander,” Tigh said heading off to carry out the order and inform the pilots who would be on patrol leaving Apollo and Starbuck still there.

“You think that’s wise, not saying anything?” Starbuck asked a bit unsure.

“Yeah, panic among the people is never good thing. The last time it took a while for it to die down,” Adama said.

Apollo was not sure he understood but would stand by his father’s decision. He hoped they wouldn’t encounter another Cylon for a long time.

End part 2

Continued in part 3

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