Disclaimer: I don't own Mass Effect, and am not making money off of these stories.

That said, the world these hypothetical train-wreaks of a story take place in is AU, and anyone expecting sanity or canon should flee far away. The idea for these stories came from playing Mass Effect 3, and my realization that EA didn't lay on the Messianic overtones nearly enough [/Sarcasm]. To correct this, I have decided to make this series of barely connected stories based on a universe where Shepard gains near omniscience from using the Beacons.

Text key

"speaking" "thinking" "Reaper speaking" -Scene info-

-Chapter 4; Naval Dogma-

-Chapter 4.1; The True Threat-

"Tim, I have a question for you."

"Shepard, you're free to use either my name or my title, but don't mock me by shortening my title to a nickname. We aren't friends."

Shepard continued on as if The Illusive Man hadn't spoken. "Is the SR-2 really still a frigate? When you rebuit it, you doubled its mass, we added multiple badass battle upgrades, and its going to be used as a mobile battle center during the Reaper invasion. Those aren't really frigate things, and I need to know my ship's technical classification for my tax return."

Tim took a heavy drink of scotch to fortify himself before speaking again. "The SR-2 was made to be a specialized stealth transport for your specific needs. You are right that it does not fit into the typical support or reconnaissance roles of typical space frigates, instead leaning more toward a troop transport role. Is that an option?"

"Nope. It only has agricultural, capital/dreadnought, carriers, cruisers, and frigates. Not even a blank line for other. That's just rude."

"Shepard, might I dare to ask why you even need to file a tax return?"

"Weapons and armor for Specters are tax deductible."

"…allow me to rephrase the question; how were you paying taxes while you were dead? How are you paying taxes now when we're the ones paying you?"

"A combination of shadow bankers, good investments, and using my Specter status to get myself listed as operating deep undercover so I still got paid by the Citadel."

"…Why do we even pay you? You have more funds in your bank than the whole of Cerberus."

"Because you know that the moment you stop bankrolling me, I split and take everyone on the Normandy with me?"

"You drive a hard bargain, Shepard, but we both know you won't follow through. The council would never let you run free to cause havoc fighting the collectors and preparing for the Reapers. You know I'm your only choice to save humanity."

-Admiral Hacket's office-

"And that's when I left Cerberus, removed their logo from the Normandy, stopped to pick up Ashley, grabbed some to-go from the Citadel, and came here. Just wanted to let you know before I started causing havoc and preparing to fight the Reapers."

"I appreciate your honesty Commander, but that can't be public knowledge. What do you want the people to hear as the official statement?"

"I faked my death, infiltrated Cerberus, came back to the alliance with a new ship full of other undercover agents, all without having to requisition any funds from the Alliance or the Citadel."

"… that is a convincing argument and fits what's in the books. Welcome back, Commander. What's your first order of business?"

"Figuring out my taxes, and for that I need more ship types. Why isn't there a ship type dedicated to safely moving troops and supplies? I'm talking military grade here, blockade runner levels. Sell 'em to the military as the answer to antai-air emplacements, they we can still move people around when the Reapers are sieging a planet."

"It's not that simple, Shepard. The Turians set the military doctrine of the Council, and they're still wary of large scare ground warfare from the days of the Krogan Rebellion. The designs would have to be made from scratch, and we don't have that kind of time. The Reapers are arriving in a little over six months, we have to make do with what we have or retrofit the ships without drawing suspicion."

"Fine then, what about dedicated bombers? Maybe load them with flares to overtax the GARDIAN systems, or better yet, make missiles that activate their thrusters when they hit an enemies' kinetic barriers, that would be a good idea."

"R&D developed those, but the council decided to ban them. The Salarians calculated that there was a point one percent chance that the missiles would explode when they were fired."

"What about making cheaper, VI controlled fighters to make opening for the human fighters to take down ships?"

"Protests against the geth made the council decide to ban any computer controlled autonomous craft."

"Remote control?"

"Takes too long to communicate in a combat situation."

"What about different ship shapes then? Why don't we make carrier ships more round, more like a battle space station?"

"No one's willing to invest in something that hasn't been proven, and a whole space station would take too much Element Zero to move effectively."

"Damnit! Why can't anyone else in this universe think outside of the box?"

The admiral placed a consoling hand on his shoulder. "There there, Shepard. It's not so bad. Sure, practically everyone in power is either incompetent, impotent, belligerent, blind, or entirely incapable of seeing the bigger picture, but at least that gives you all the more opportunity to shine! Just imagine, if the council took your advice and used their brains, then you wouldn't be nearly the hero you became."

"Is that the official stance of the military?"

"No, but they do say that a good army is nothing without a good commander."

Shepard stood up with renewed confidence. "By Golly, Uncle Hackett, you're right! I'm going to give those ruffians the what-for!" The Commander strode out of the door, then returned in under ten seconds. "On second thought, why should I waste my genious plans on the collectors when the Reapers are on our doorstep. I'm gunna go take out Harbinger." Shepard left and returned after five seconds. "On third thought, why do I even need to bother with the Reapers or the Collectors when the thing controlling them is right there on the citadel. I'm going to go give that program the what-for. Then I'm going to take their ships, give them to the alliance, and make them recognize that there needs to be more ship types on the tax form!"

Hackett just shook his head as Shepard walked out and didn't immediately return. He opened a line to call for his intern. "Mr. Scott, could you please add a reminder to watch the evening news. Clear my schedule and prepare a bottle of scotch. Shepard is going to do something again."

The young man's voice conveyed genuine sympathy. "I understand, it will be ready, Sir."

-That Evening-

The camera panned to an attractive Asari sitting at a desk double checking her make-up on her omni-tool. "Good evening, this is Citadel News. Our top story this evening is the mysterious power outage that affected the Citadel for from three to three thirty in the afternoon, galactic standard time. This station-wide power outage is the first that the Citadel has ever experienced. The mysterious Keepers have always kept the station running smoothly, but they all died in the minutes leading up to the power outage. We're here on the scene with the Keeper expert, Chorban. It's good to have you on the show, Chorban. What's your take on the situation?"

The Salarian quickly closed a tab on his omni-tool and coughed nervously. "As everyone knows, there is not much known about the Keepers below the surface level. However, I managed to acquire data that leads me to believe that they were bio-engineered from a now-extinct race millions of years ago. The data indicates that they were created by the same civilization that created the Citadel to respond to some signal every 50,000 years."

The Asari widened her eyes in exaggerated disbelief. "Are you saying that the Protheans created the Keepers?"

Chorban looked away. "I am not an expert on the Protheans, so I reached out to Dr. T'soni for her thoughts. She passed along some interesting data. If her data is correct, then the collectors are Protheans who underwent the same sort of bio-engineering. With this data, I constructed a hypothesis, the Keepers and also the Collectors are slaves of an ancient race of highly advanced beings."

"And what are these beings?"

"I pondered that for a long time, but then the answer became clear. The Keepers run the protein vats, why? To create food for their masters, of course! The masters of the Keepers and the Collectors are highly advanced micro-organisms, most likely viruses. Every fifty thousand years, they give the Keepers the signal and are released to feast upon the galaxy and evolve."

Silence filled the room. The Asari looked to the camera before slowing pulling out a plague mask and putting it on. "That seems rather far-fetched, Dr. Chorban; what evidence led you to this conclusion?"

"It's simply the most efficient answer to the questions. We this elegantly explains the modifications, the fifty thousand year signal, the lack of diversity in a galaxy as old as ours, all without having to bring in absurdities like ancient robot space-ships with mind control powers and no sane reason."

"it still seems odd that a mere virus could be so intelligent."

"It's simply logical. After all, micro-organisms existed for millions of years before any larger beings came onto the scene. It's simple logic and evolution that they would eventually rise to this point with all of the time that has passed."

"What would it mean that the Keepers died, then?"

"Obviously they became unnecessary. The only sane explanation is that the Master Viruses ascended to a higher plane of existence. Either that, or they found a better race, in which case all of galactic society is doomed if we don't take immediate drastic measures to fight this enemy. First we'll need to-"

The Asari glanced at an invisible clock and smiled. "That's all the time we have for today, thank you for coming on Dr. Chorban. In other news, one Citadel pet owner decided to teach their pet an unusual trick. Captain Bailey of C-Sec trained a pyjak to check for weapons."

The news report closed itself, and Hackett turned to regard the sobbing commander at his side. "You're right, it does make more sense than an AI killing all organic life to prevent AIs from killing all organic life."

"That's the problem! What really happened is so stupid! The donation of all those ships wasn't even recognized as charitable! And then they said that they're going to have them all torn apart so they don't have to consider different ship types! That does it; I'm going back in time to stop myself from destroying the Reaper Program! Just a few presses on the keyboard, and it'll make my new ship types, then they'll have to change the tax form." Shepard pulled himself together for a second before breaking down again. "But the only way to time travel needs the Reaper program to run it! Why don't I think before I act!"

Hackett patted the man-child on the shoulder. "There, there. We can still fill that shuttle with antai-matter and send it through the Omega-4 Relay, if you want. When all else fails there's still expl-ACHOO!"

Shepard looked up from his moping. "I told you it wasn't a good idea to drink scotch old enough to gather dust."

"Very funny, Shep-Aahchoo!"

Suddenly concerned, Shepard activated his omni-tool and scanned the admiral. Within a few seconds the results came back. The near omniscient Commander froze. "They're real…"

Chapter 4 end!