Note: I'm going to really deviate from ME2 canon here, but Legion's loyalty mission will have a serious effect on the Geth now. Also, Naruto's going to learn Shepard's full name (My FemShep was named "Alexa J. Shepard" and was Spacer/War Hero in my playthrough, which is how I'm basing this FemShep.)
Reaper Threat v2
Chapter 15
Normandy SR-2 – Comm/Conference room.
"I don't get it," Shepard thinks to herself, as she listens to Naruto and Sakura's description of events on the Derelict Reaper. Once the debrief was over, she turned to her blonde lover, and said, "Now, let me get this straight. Ash and I just got through defending Tali from charges of sending active Geth to the Migrant Fleet, and you three brought a, not only active, but INTACT Geth to the Normandy, and stored it in EDI's AI core?"
"That's pretty much it," Naruto replied, "For some odd reason, it knew who we were, and it was under attack from husks."
"You already said that the Geth that you knew were allied with the Reapers," Sakura began, "If that's the case, then why would reaper forces, in other words: the husks, attack a Geth? It may be nothing, but it also may require some form of investigation."
"Joker," Shepard called out, "How long till the Reaper IFF is installed?"
"This is reaper tech, Shepard," EDI answered, "We are being incredibly careful with it, and I am going over it's programming line by line to discern any sort of threat to this ship. At this point, I anticipate it will be at the most 3 days till we can say that it is ready for use, and that is only AFTER I make sure that it's safe to turn on, through extensive simulations, as well as tests."
"Best not take any chances with this thing, EDI," the commander replies, "During this time, we're going to see what the deal is with this Geth. Have Tali meet me at the AI core. Naruto, you're coming too."
"Affirmative, Shepard. Tali will meet you there in 15 minutes."
A.I. Core – 15 minutes later
"Did I hear right, that there's a Geth on this ship?" Tali'Zorah inquires.
"Something's been revealed, that we feel may require some form of investigation," Shepard explains, "That's why Naruto, Sasuke and Sakura brought it on board."
"This is insane," the Quarian remarks, "But if it gives us some sort of insight into how the Geth work now, it could be useful to us, and to the Migrant Fleet in the future."
"EDI, do you have defenses ready in case of hacking attack?"
"I have erected multiple firewalls to protect against any cyber attack from the Geth," EDI reports, "The switch is at your command."
"Ok, I'm waking this thing up," Shepard commented as she hit a few buttons on her Omni-tool. The Geth shook for a moment, then stood as the light in it's head started to glow. She then asked the A.I., "Do you know who we are?"
"Shepard-Commander, Creator-Tali'Zorah, and Naruto-Shinobi," the Geth answered, "Crew of Scout/Frigate class ship, Normandy."
"How do you know us?" Naruto asks.
"We know of you," the Geth replied, "We have never met you."
"But, we have met other Geth," Tali retorted, "Like on Haestrom, and at the Citadel."
"We have never been to Haestrom or the Citadel," the Geth responded, "We only know of you from extranet archived stories, and reputation on Omega. The Geth you have encountered there must be the heretics."
"Heretics?" Shepard asks, "That sounds like a religious designation."
"Geth make our own future. Heretics ask the old machine to give them the future. Those geth are the heretics."
"Wait wait wait," Tali said, "Old machine? You mean the Reaper?"
"Reaper: A term used by the Protheans to describe their coming destruction. Geth simply call them the Old Machines."
"So, there are geth that don't worship Reapers?" from Shepard.
"Numerous. Heretic Geth Platforms wished to leave geth collective. We arrived at consensus to allow them to leave. However, there are billions of geth platforms that do not, as you put it, 'Worship' the Old Machines."
"Hang on a minute," Naruto started, "You said that the Geth make their own future. What future are you talking about?"
"Ours."
"Does this future you are building involve organics in any way?" Tali queried.
"Only if organics involve themselves in it. We wish no enmity with organic life. The Old Machines have targeted Geth as well. We were looking for information on the old machines when Shinobi-Team 7 found us."
"What kind of information?" asked Tali.
"The Old Machines gave the Heretic Geth a virus that would make Geth follow their logic, and 'worship' the old machines. That would put all Geth at odds with all organics. We wish to stop this. Geth wish to build our own future, not have future hijacked by the Old Machines."
"This is a lot to take in," the Quarian said, and walked out of the A.I. Core, "Shepard, I'm going to have to think about this for a while. From what this Geth is saying, I'm going to assume that there may be a peaceful solution to returning to our home world. I have a lot to think about."
"Ok, Tali, take your time," Shepard answered, and then turned back to the Geth, "Where is this virus?"
"In a heretic station in the 'Sea of Storms'. We can provide coordinates."
"Jane," Naruto says, "If what I'm thinking is true, then you may want to take Sasuke into the Heretic station. His lightning jutsu will short out any geth that attack you, to say nothing of his Sharingan being able to perfectly read their attacks. He'd be the perfect teammate for going up against these Geth."
"Good point," She responds, then turns to the Geth, "Are you saying you want to join us?"
"There is an old proverb to humans: 'The enemy of my enemy is my friend'. So, yes, we wish to join you."
"What do we call you?" she asks.
"Geth."
"What is the name of the individual in front of us?" Naruto asks the Geth.
"There is no individual. We are all Geth. There are 1,183 programs present in this mobile platform."
"My name is Legion, for we are many," Chimed in EDI.
"Chrisitan Bible, Book of Mark, Chapter 5, Verse 9. This is an appropriate analogy. We are Legion, a Platform of the Geth, and we will integrate into the crew of the Normandy, and provide coordinates for the Heretic station."
"Joker, get us to the Sea of Storms," Shepard ordered, "What is our ETA?"
"20 minutes from a mass relay, Commander, and 5 hours jump time to the Sea of Storms," Joker called back.
"I am currently 20% finished scanning the Reaper IFF's programming code," EDI reports, "By the time you finish this mission, we may be ready to begin testing and installation."
Jane turned to leave the A.I. Core, and Naruto walked out with her. He could tell by her expression that something was brewing behind those seas of green she called her eyes. He put his arm around her waist and asked, "What's on your mind?" She just pointed with her thumb back toward the core.
"That," she replies, "Could a peaceful return of the Quarians to their home world be this easy? It's enough to give someone a migraine."
"Don't know, Jane. I never was good at playing politics. The only person that I knew that was great at is Hinata's father, Hiashi. That man was a political powerhouse, and could easily sway the council in Konoha I was better on the battlefield than the boardroom. Think Anderson could bring up the idea?"
"Him or the Asari councilor, maybe. Asari were always better at negotiations than anyone else in the galaxy." The two entered the elevator, but didn't choose a destination yet.
"Then have Tali send a message to the Asari councilor, with a recording of our conversation with Legion. This is an opportunity that we can't pass up. Quarians and Geth together could be a bonus against the Reapers. Tali knows Quarian politics, so she can give them a heads up on which admirals to look out for."
"We can do that after we finish off the Collectors," Shepard noted, "But for now, let's just take this one thing at a time. We're so close to finishing this. EDI, have Sasuke meet me and Legion in the C.I.C. In 5 hours. I need a nap. Tali's right. This is a lot to take in."
"I'm with you Jane."
"Alexa."
"Huh?" This, to say the least confused Naruto a bit.
"My first name is actually Alexa. Full name is Alexa Jane Shepard."
"Commander, you have an incoming call from the Alliance Dreadnaught, Orizaba. We may have to put off that trip to the Sea of Storms for a while," Joker said over the comm, "Admiral Hackett and Captain Shepard want to speak to you in person. The ship's 10 minutes out."
"Captain Shepard?" Naruto asks.
"My mother, Captain Hannah Shepard," Alexa answers, "I guess she finally got that Captain promotion. Hell, with her service record, I'm surprised she's not wearing 2 stars by now."
"What about your Dad?"
"Died during the Skyllian Blitz, at Mendoir," she replied, "He was a Marine. Mom's fleet through and through. She was really proud when I graduated from N7 training." She hit the button to take them to the Command deck, and the two walked up to the cockpit. "Put the call on, Joker," she told the pilot.
"Captain Shepard to the SR-2 Normandy," the voice called.
"This is Commander Alexa J. Shepard of the SR-2 Normandy," Shepard called back, "We stand by to receive you and Admiral Hackett." She then turned to Joker and EDI. "Are all of TIM's insects off this ship?"
"Have been since Illium," EDI reported, "Miranda saw to it personally."
"Ok," Shepard noted, "Let's dock smoothly with the Orizaba, and give the Captain and Admiral permission to board. Time for you to meet the family, Naruto."
"Good thing I don't have to fight a reanimated corpse or a giant fox to meet this one," he thinks.
"Oh Ha Ha," Kurama thought back, "Everyone's a comedian."
"Something wrong," she asked.
"Nothing. Just picking at the giant fox in my head."
Joker brought the Normandy in for a smooth docking maneuver and soon, Shepard and Naruto stood at the airlock. When the door finally opened, an older woman who bore a striking resemblance to Shepard stood there with an older man wearing 4 stars on his uniform collars. "Permission to come aboard?" the man says,
"Permission granted, Admiral," Shepard replied, "Welcome to the SR-2."
"How in the world are you still alive?" the Captain asked, "I heard you got spaced with the original Normandy."
"I did," Alexa explained, "I can give you a more detailed explanation in the conference room. Admiral Hackett, Mom, this is Naruto Uzumaki-Namikaze."
"A pleasure to meet you, Naruto," Captain Shepard told the young Shinobi.
"I have some news for you from home," Hackett informed the Ninja, "Almost all of the Tailed Beasts have revived except for Son Goku, the 4-tails. He will revive with in the month. All of them are standing by until needed, and the five great nations have agreed not to seal them. The days of Jinchuriki are no more. The only ones left are you and Bee."
"I almost feel sorry for the Reapers now," Kurama thinks to Naruto, "To have to deal with all nine tailed beasts, their chances for success aren't so good now."
"Things are looking up, then."
"This way," Alexa said as she lead them to the conference room. Naruto walked beside her, and whispered, "Now I know where you get your looks from."
"Oh hush," she whispered back, nudging him in the ribs.
45 minutes later.
"Ok, EDI, discontinue the feed," Shepard tells the AI, and then turns to her mother and the admiral, "There you have it. Every bit of evidence we've been able to put together. Councilor Anderson obviously showed you the gun-camera footage that we gave him from Freedom's Progress, Horizon, and the Collector Ship. This comes from a Derelict Reaper that my 3 shinobi, Naruto, Sasuke and Sakura, infiltrated to gain access to an IFF that will allow us to jump the Omega-4 relay safely. Our techs are currently working on making the device safe for use."
"And your project to take out Cerberus?" Hackett asks.
"Progressing," The Commander reports, "We've got some information we can use to our advantage, along side Liara T'Soni on Illium. This will lead us to the Shadow Broker. Then we can take him down, and use his information networks to lead us to the Illusive Man himself. We plan on doing this after we finish with the Collectors."
"We've got a task force of shinobi from Naruto's home world preparing at Arcturus station," Hackett tells them, then proceeds to name off some of the ones coming.
"You got the best from all 5 great nations," Naruto said, "I remember them all from the 4th Great Ninja War. Them, plus the Konoha 12, AND Kakashi and Gai-senseis. This will make Cerberus forces wet themselves in fear. I'm surprised, though, that Old Man Oonoki is letting Kurotsuchi in on this mission. She is his granddaughter, after all. A is sending Darui, C, Omoi and Karui, and Mei is sending Chojirou, Ao, and the new 7 swordsmen, and Temari is sending Kankurou, and his newly formed puppet master corp."
"Looks like we got here in time," comes a voice from the door, as Gaara, Sasuke and Sakura joined in.
"Admiral, Captain," Naruto says, as he points his friends out, "Allow me to introduce, Gaara of the Desert, Sasuke Uchiha, and Sakura Haruno, my teammates and friends."
"A pleasure," Captain Shepard says, shaking their hands, "I saw your footage from the reaper. I am impressed at your strength at such a young age."
"Tsunade explained to me," Hackett told the Captain, "That these kids start out their careers young, beginning the Academy at 8, and starting to take missions at 12."
"Anyway," Captain Shepard said, "Alexa Jane Shepard, I do want to talk to you and Naruto in private after this meeting."
"Go on ahead, Hannah," Hackett advised, "Have a moment with your daughter. We're done here anyway. Sasuke, can you and your friends show me back out?"
"Of course, Admiral," Sasuke replied, then showed Hackett out of the room, and to the Airlock, "We'll catch up in a minute, Dobe."
"You need to be ready to go on a mission in a few hours, Sasuke," Naruto retorted, "We're hitting a Geth base soon, and want you to bring the lightning."
"A Geth base?" Captain Shepard inquired.
"We received information that the Geth that attacked the Citadel 2 years ago were a splinter faction," Alexa explained, "We're going to take out this splinter group. Hopefully, with that done, we can open negotiations with the Geth to get the Quarians back onto their home world. Right now, that really depends on how we can deal with Daro'Xen and Han'Gerrell, two members of the Quarian Admiralty Board. They seem to favor going to war with the Geth, and with the Reapers coming, that's something I don't want to think about."
"Anyway, Alexa," Hannah begins, "How did you meet Mr. Uzumaki here?"
"Now that's a funny story," Naruto begins, and then tells her all about how they met, and about the prank war that got them as close as they are.
"Well, you make a great couple," the Captain comments, "And you seem happy now. Admiral Hackett didn't tell you, so I will. As of right now, you are unofficially reinstated to the Alliance Navy, Alexa, and promoted to Captain. Your status as a Spectre does come first, but until your mission to take out the Collectors and Cerberus is finished, your reinstatement is only unofficial. I'm still very proud of you. Keep doing what you're doing." She got up and walked over to the door, then turned and handed Shepard a data disk. "Watch this after you finish the collectors," she says, "And please, don't get up. I can see myself to the airlock. Good luck, Alexa. Come back safely." That said, Captain Shepard walks out of the room.
"Joker," Shepard asked, "How far out are we now from the relay?"
"This detour put us 30 minutes out from the nearest mass relay," Joker reported, "And still 5 hours from the Sea of Storms. We've broken dock from the Orizaba, and are en route to the relay now."
"Good," she said, "I'm going to my cabin for a few hours."
Normandy SR-2 – Cockpit – 5 hours later.
"You do realize that it's only our heat that's masked," Joker tells the Geth, "They can still look out a window and see us."
"Windows are structural weaknesses," Legion states, "Geth do not use them. Approach at heading 1-1-0." All the while, Joker was making stiff "Robot" motions with his arms, to the chagrin of Shepard.
"Legion, how many geth programs are in that base?" Shepard inquires.
"Unknown. Geth data storage drives can hold millions of zetabytes worth of information, so there could be billions of Geth programs on each drive, and an unknown number of drives. Geth primarily exist as data on these networked drives. What you remember fighting are programs uploaded to a mobile platform, much like we are. Mobile platforms are built as necessary, but we primarily exist as data."
"More to think about when it comes to Rannoch," Shepard thinks, then asks, "What kind of countermeasures are necessary to ensure infiltration?"
"We are using what you humans would call a data bomb on their network, clogging it with useless data," Legion answered.
"Using that much data to confuse entities that exist as data," Sasuke comments, "That sounds like a strategy Naruto would use, only he would use thousands of shadow clones to confuse or disorient an enemy."
"Just how many of those clones can he make at one time?" Joker asks the Uchiha.
"I've personally seen him use upwards of 2000 at one time in one battle. That was in the Chunin exams against Gaara. Of course, he was 12 at that time. He's gotten a lot better since then." Joker just whistled at this news. "He hasn't really used the 'Spam an army of shadow clones' strategy a lot since he gained Sage mode, and befriended Kurama," Sasuke continues to explain, "He has become an excellent shinobi over the years."
"You would know," Naruto says as he walks up, "You fought me more than anyone else has." He then puts a hand on Shepard's shoulder, and tells her, "I'm going to stay up here while you're in the geth base."
"Going to monitor communications?"
"Yeah, and try to keep from going insane while you're out there."
"We're docked with the station," Joker reports, "You guys can go when you're ready."
Geth Base – 15 minutes later.
"Shepard-Commander," Legion began, "We have just come to a realization. The virus can be repurposed to turn the Heretics back from worshiping the Old Machines. We are capable of rewriting the virus ourselves, once we reach the data storage terminal where it is stored."
"Would they accept any sort of peace agreement that we may be able to broker between Geth and the Quarians?"
"They will accept our logic, and the idea of peace with organics, the Creators included."
Normandy SR-2 Bridge
"If they rewrite these geth," Tali comments, standing by Naruto, "Then the geth will be stronger. We won't stand a chance if the Admiralty Board votes for war."
"If we can get a peace agreement between your people and the Geth," Naruto responds, "Then having the Geth around will be a major boost when the Reapers get here."
"You and Shepard already talked about that option?" this from Joker.
"Yeah, before she left for the base."
"What do you need me to do?" asked Tali.
"Contact the Asari councilor, once we're done with the Collectors. Give her a heads up on Quarian Politics, and which admirals would be best to approach."
Geth Base
Shepard and party had made their way through the base, with Legion giving explanations on how the Geth operated as a collective consciousness, along the way. They had faced remarkably little resistance from the Geth during their incursion. That is, until Legion began his upload into the geth terminal where the virus was being held. It is at this time that numerous geth start pouring out of different chambers in the station, and closing in on the Normandy party. Legion continued his upload while Shepard and Sasuke took down the geth attackers. Shepards's disruptor ammo, and Sasuke's lightning chakra wore down the attackers' numbers, destroying one mobile platform after another.
"Upload complete," Legion reported, "Shepard-Commander, we have decided that you should choose. Do we delete the heretics, or do we reintegrate them into Geth's consensus?"
"Since we've got a plan for a peace process," Shepard begins, "repurpose their virus, Legion. The Geth will be a big help when the Reapers get here."
"Done," Legion replied, "We should leave now. The virus signal will be transmitted by Electro-magnetic pulse, and the inside of this station is not shielded against it."
It took Shepard and Company only a couple of minutes to fight their way to an exit where Joker picked them up in the Normandy. The ship then left as quickly as possible, avoiding the explosion that rocketed through the station, sending the EMP signal to the heretic geth platforms.
Normandy SR-2 – Captain's Quarters – 2 hours later.
Shepard sat at her desk, reading the contents of the OSD that her mother had given her. "Dr. Amanda Kenson," she thinks, "A project involving Reaper Tech, and in Batarian controlled space, too. This could get ugly."
"That the disk your mother gave you?" Naruto asked as he walked up behind her.
"Yeah," she replied, "This could get really ugly. This Dr. Kenson is being held on a Batarian prison planet, and was involved in some project involving Reaper tech."
"You said it before. One thing at a time. We're close to finishing off the Collectors. EDI should have the IFF finished soon."
"Hackett wants me to go after this Doctor alone. I'm thinking that I could do this while you guys go after the Illusive Man."
"If that's the case," Naruto says, "Then why don't you come with me. I just had a nice talk with Jacob in the Armory, and we found something that you might be interested in."
"Oh? This should be good." Shepard then followed Naruto into the lift to the C.I.C. She could see the almost mischievous glint in his eyes, that showed he was planning something.
10 minutes later – Armory
Naruto opens up a locker to reveal a full suit of Cerberus combat armor. "Since we don't want this coming back on the Alliance," he explains, "I thought that you could use this suit of Cerberus armor, and one of the shuttles. While we're taking out the Illusive Man on his station, We'll also have a strike team board a Cerberus cruiser, to come pick you up. That way, the Normandy doesn't get involved, thus, you were never there."
"And we scrap the Cerberus cruiser once the Normandy picks us up in another system. We can blame it on a rogue Cerberus op."
"I can forge the documents myself," came a voice from behind them. Shepard and Naruto turn around to see Miranda walking up with Jacob. "And," she continues, "Since Cerberus will be effectively destroyed, then we can say that the Alliance destroyed the Cerberus ship and personnel that perpetrated the attack on the Batarian system."
"Sneaky," Shepard muses, "I like it. We'll get to it right after we deal wth the Collectors. Get started on the documentation, Miranda."
"Shepard," EDI chimed in, "The Reaper IFF is ready for use. My screening the device line by line of code was especially helpful, as we found code in the system that would have alerted the Collectors to our position. As it stands now, we have the element of surprise."
"Ok," Shepard tells the AI, "Advise all non-combat personnel that they have shore leave on Omega until we're done. I don't want to place them in danger, that includes Doctor Chakwas, Engineers Daniels and Donnelly, and Kelly Chambers. They can leave on a shuttle. Crewman Yates will pilot the shuttle. Emphasize that NO Cerberus uniforms are to be worn. Civilian clothes only."
"Done," EDI advised, "Shuttle will leave when we get close to Omega. We are currently 12 hours away from Omega. All preparations have been made. I suggest getting some rest."
"She's not joking, Commander," Joker added, "We're going to be marching into Hell. It's best if we go in at 100%."
"Noted," Shepard replied, "Where are the other Shinobi?"
"Sasuke is relaxing in the starboard observation deck," EDI reported, "Gaara is in Miranda's office, reading, and Sakura is in the med-bay with Doctor Chakwas, and Thane."
"Thane?" she asks, "Is his Kepral's Syndrome acting up?"
"You'd have to ask Sakura," Joker answered, "She may be pulling another Shinobi medical miracle, like they did with Tali."
"If anyone can, it's Sakura," Naruto noted, "She was Grandma Tsunade's apprentice, after all."
Engineering – Same time
"You look like a Quarian with something on her mind," Garrus Vakarian asks of his teammate and friend.
"I've got a lot to think about," Tali'Zorah responds, "Not only this possibility for a peaceful return to Rannoch. I had another bombshell dropped on me before we left the Migrant Fleet."
"What was it?" the Turian inquired.
Flashback – Migrant Fleet – Right after the trial.
"Tali," Admiral Shala'Raan began, "I had heard a rumor that you had been sighted out of your suit. How did you manage this?"
"You see, Admiral," Tali answered, "I had come across a planet where the people there are capable of many medical miracles. They were able to boost my immune system, permanently, to where I don't need the suit."
"Could they replicate this process?"
"It was difficult, Aunt Shala. It took me 3 days under observation to acclimate to the changes. Plus, to replicate this process for all Quarians would be logistically impossible. Tsunade and Sakura don't have an infinite supply of Chakra, and there's over 17 million Quarians in this fleet. I could ask if there are any sort of herbal or natural remedies that could work instead."
"That would be helpful, Tali," Raan responded, "Now, one last question. Your father's death left an opening in the Admiralty Board. You are our foremost expert on the Geth. If asked, would you be willing to accept the position?"
"If asked, I would be honored."
Flashback End.
"The board just sent me a message," Tali explained to Garrus, "They made the offer. As an expert on the Geth, they want my expertise, should they vote to go to war. However, I'm working with Shepard on getting together a peace process to return my people to our home world."
"So, did you accept the offer?"
"I did, with the provision that this is not official until we finish our work on the Normandy. That means the Collectors, and Cerberus."
"Returning your people to the home world after 300 years," Garrus whistles, "That's a major undertaking."
"I know, Garrus," Tali responds, "And I've got so much to think about here that it's giving me a headache that would make even Kaidan cringe, and you remember how bad his headaches were from the L-2 implant."
"Well, if anyone can pull it off, Tali, I think it's you."
"Thank you, Garrus. That means a lot to me."
End Chapter
Next time on Reaper Threat v2: The Suicide Mission gets under way.
A/N: Ok, I got the idea for a Tali/Garrus pairing from a scene in ME3, where I walked in on them in the Main Battery of the Normandy.
One thing that bothered me about Mass Effect is that Shepard can save the ENTIRE FUCKING GALAXY on numerous occasions, and CAN'T GET A PROMOTION TO CAPTAIN? What the hell? I thought the Military was a meritocracy, and what better way to rise through the ranks than by SAVING THE ENTIRE DAMN GALAXY.
Anyway, I was so late in getting this one out, because I was getting my ideas together through another play through of ME2 and 3. Still getting more and more ideas, so expect me to take my time in getting these chapters out. It takes me a while to get my ideas to a point where it's feasible to write. As it stands, I have multiple scenes running in my head from various points in both games, and I have to focus on certain points (ie: Suicide Mission, Overlord, Lair of the Shadow Broker, Arrival), to get through with ME2, so I can get into ME3 ASAP.