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Welcome to Season Three of Neon Genesis Evangelion: Last Best Hope. The events chronicled here take place after the 1st season of the TV series, and the End of Evangelion Movie, as well as the events that took place in "The Awakening." The 24 part second season.

Episode 3:01 Upgrade

Presumed date is June 9th, 2019

Misato sat at the head of the briefing table, her laser pointer working the projection screen.

"So, we know we need to salvage a Magi System in order to access the Global Military Satellite network," she was saying. "The two most logical choices are Beijing, or Matsushiro, as they are the closest. Matsushiro is the target of preference because it's closer, and recovery time is likely to be shorter."

"However when Lilith's body was decomposing after Third Impact, part of her arm fell on that region, and there was extensive damage to the base. We weren't able to salvage anything from there before, but we didn't ever consider sending an EVA or a Cherub to assist in the recovery," Ritsuko said.

"So, we send a force of Cherubs to help the recovery teams breach the facility, and then recover the Magi units there. We bring them back here and install them in the control center, with as much of the hardware as we can salvage from the Matsushiro base installed intact. What's the soonest you think you can have them up and running, once you get them back here?" Misato asked.

"Depending upon how co-operative the personalities within the three units are, we should be able to get them up and running within a week. Provided that their hard drives are still good. If they've crashed, we'll have to see if we can find replacements, and that won't be easy."

"Okay, so, we'll have Aida and Suzuhara go with the crews to handle recovery of the Magi. In the meantime we'll load up the last four EVA transports with Cherubs and send them to Germany. Asuka says that Germany has plenty of Aviation fuel, and even some aerial refueling tankers. We'll send a couple of our own up, and hope that they figure out what we're doing when they take off. When the transports return, we'll send four more units, giving Germany a total of eight. That will leave us with the two EVA's, and eight Cherubs of our own," Misato said.

"Seven," Ritsuko corrected, "Keller was killed."

"Jeez, how could I forget that," Misato said, resting her head against her hands.

"So, Ritsuko, the question becomes, do we need more Cherubs to secure the cities we know are inhabited?" Misato asked.

"I don't know. We have twelve empty growth chambers below now; I hadn't thought we would ever need more than 16 Units. We could always start the next group of twelve, and then, if we don't want them, flush the tanks before they reach the third trimester."

"Okay. That sounds like a plan, better to be safe than sorry, I suppose. So have you decided if you're going to take Commander Bergs invitation to come to Germany and see their weapons?" Misato asked, recalling the message that Asuka had conveyed from the new Berlin NERV Commanding Officer.

"Oh, I'll go, but I want to get the Magi up and running first. Then I'll go."

"Okay, I need to call Aida and Suzuhara to let them know we've got a mission for them. Do you have you're recovery team picked out?" Misato asked, picking up her phone.

"Yes, they're on standby now, just waiting the word," Ritsuko said.

Misato nodded and dialed Kensuke's house.

"Aida here," he answered.

"Aida, Misato. I want you and Suzuhara to accompany the recovery teams to Matsushiro to help them dig out and retrieve the Magi system. Get him, and get in here quick. The teams are leaving in an hour."

"Yes, Ma'am. I'll go get Toji now. He and Hikari are over at Shinji and Asuka's."

"So they finally decided to surface did they?" Misato laughed.

"No, but Toji and Hikari didn't give them a choice. Hikari took them breakfast in bed this morning, and needed Toji for an escort. She decided last night that they had had two full days all to themselves, and it was time they came out of seclusion. Besides, she was gonna go nuts if she couldn't talk to Asuka after all these years."

"I can understand that. Anyhow, get Suzuhara and come on in, we'll need you guys to clear some debris," Misato said.

"Roger Commander," Suzuhara said, hanging up.

###

"No-chan?" Kensuke called.

"Yes Ken-chan?" Nozomi answered.

"You want to go over and bug Shinji and Asuka with Toji and your sister?"

"Sure, sounds like fun, lets go," she said, looping her arm through his, and dragging him out the door.

Moments later they were jogging across the deck, and up to Shinji's back door. They knocked briefly before opening it and walking in. Toji and Hikari were sitting at the kitchen table, talking to Shinji and Asuka. The new couple was still dressed in their pajamas. Or more precisely Shinji's pajamas. Shinji was wearing the pants and a white undershirt. Asuka was wearing the pajama top.

"Kensuke, come on in," Shinji said, waving Kensuke and Nozomi in, and motioning them to have a seat.

Kensuke sat down, Nozomi following close behind, and turned to look at Shinji and Asuka. They weren't sitting in the normal chairs that surrounded the table. Instead Shinji had pulled the small bamboo couch, covered by a thick cushion, over to the table, and he and Asuka were curled up together on it.

Kensuke smiled at them.

They were holding hands, and even when they reached for their tea, they kept one set of hands clasped together.

"Now Asuka, what is the story with your hair?" Hikari asked.

Asuka smiled, and ran a hand through the lions mane of hair that was puffed up around her, glowing in the morning light.

"Baka Shinji. He messed it up. It's okay though, I told him if he's going to mess it up he's got to brush it out," she smiled up at him.

Kensuke swore and Toji laughed.

"Dude, that's a week you owe me," Toji said, pointing at Kensuke. For his part Kensuke could only nod.

"What?" Hikari asked.

"I bet Kensuke that Asuka would be calling Ikari 'Baka Shinji' within a week. He's got to clean my uniforms and boots for a week now."

"Speaking of Uniforms, Misato needs us to get to the base. We're gonna take the Cherubs and help out the recovery teams that are getting the Magi system," Aida said.

"Okay, but did they decide which one we're going after?" Toji asked.

"Matsushiro. But the entrance to the base is damaged, and they want us to dig it out for the recovery teams," Kensuke said.

"When do they need us?"

"Misato said ASAP. We're leaving within the hour."

"Well, we'd better get going, then, bye guys, bye honey," Toji said, bending over to kiss his wife goodbye.

Kensuke got up, and followed Toji out the door, and within a few minutes, Toji's 4Runner could be heard pulling out of the driveway.

"So what are your plans for the day?" Hikari asked the couple.

"Well, we had planned on just lying around the house, but Shinji mentioned something about a dip in the Jacuzzi, I think."

Shinji blushed, "Well, Kensuke fixed it up, before he moved out. I haven't been in it for some time, and thought it might be a good time to get back into it. I should probably call Misato though and see if she needs me for anything."

He was reaching for his cell phone, when Asuka reached over and slapped his other hand.

"No you don't, Misato knows your number, if she wants to talk to you, she'll call."

"She's right Shinji, Misato said you should take the next few days off, and she'll call you only if she really needs you. You have other responsibilities this week," Hikari said.

"Yeah, like making sure my every need is met," Asuka teased.

Shinji surrendered.

###

"Okay Aida, can you see any sign of the main shaft?" Doctor Akagi asked.

"Sort of. I think that this blur here is the most likely place," Kensuke said

"Suzuhara, can you see anything from where you are?"

"No Ma'am, I've got nothing," he said. He didn't like being here, it brought up some really bad memories. This had been where the activation test for Unit-03 had taken place. Where the Angel had seized control of his EVA and tried to kill him. Then, after he'd been trapped while eject from the Angel, he'd been crushed in the berserk hand of Unit-01 under the control of the Dummy Plug.

He didn't remember much of it, because he hadn't really been paying that much attention at the time, at least not until things went wrong. Then he was riveted to every minute detail. He glanced around. Over there was the small valley he'd entered as Unit-03 had begun walking, inexorably towards Tokyo-3.

"Doctor, Akagi, I know its' been several years, but I think I remember that valley there. If I do, then that means the entrance Unit-03 came up through is over in that depression somewhere," he said, his huge Cherubim hand pointing to a low spot in the forest.

"Okay, you two go investigate over there. After your EVA was taken over and escaped, we capped the main shaft with a thick concrete plug," Ritsuko said.

Toji and Kensuke moved over to the indicated area and began pulling up the trees that had sprouted like weeds. This area had been lightly forested before Third Impact, with several buildings on the surface, and the city in the distance, but the fall of Lilith's arm upon this area had devastated everything, making it unrecognizable.

The arm has flattened the structures, either by direct impact, or shockwave, and as it decayed into the soil, the plants had seemed to be trying to cram 20 years of growth into a single year. So now, here they were, three and a half years after Third Impact, standing in the middle of a tropical rain forest, with trees almost as tall as the Cherubim.

Kensuke's foot scuffed the detritus of the forest floor, and revealed a dull gray surface.

"I have something here," he said, bending over and starting to uproot trees and bushes.

Soon one edge of a large circle was revealed.

"This is it," he told Toji. "Doctor Akagi, we've found it."

She and a group of technicians drove their HumVee's over to the area that Kensuke and Toji were clearing, and could now make out the large circular plug of concrete. It was about as wide as a Cherubim was tall, and must have easily been twenty meters thick.

"Okay, can you two pull that thing out, or should we try to blast it. I know the engineers brought a fair amount of C-4 just in case."

"Let us give it a try," Toji said, squatting down, and waiting as Kensuke did the same.

"Ready?"

Kensuke nodded, and they thrust their fingers into the seam between the plug and the walls of the hole. They dug down, until they each had a firm grip.

"Okay, we lift on three, and toss it north. Ready? One. Two. Three." Toji said, and they tossed the heavy plug to the side, away from Ritsuko and the other personnel.

Toji peered within.

"Nothing on thermal or infrared. Lowlight is almost useless as well, no emergency lighting detected."

"Without external power to recharge them, or take over. Emergency lighting would have lasted no more than two weeks," Ritsuko said. "Have either of you memorized the maps of this place?"

"I did," Kensuke said.

"Do you think you can go down here and clear us a path to Central Dogma?"

"Yes Ma'am. Toji, give me a hand getting into this hole," he said, standing up, and gripping Toji's had, as he descended into the darkness. Toji helped, a little uneasy about entering this structure again. Soon Kensuke's Cherub was out of sight, as it dropped into the depths.

"Aida here Doctor Akagi, I've reached the first barrier at the bottom of shaft A-17. Proceeding to open the doors."

From deep within the facility, there was a loud creaking and ripping.

"It's dark in here. Deep dark. I'm gonna need that emergency source."

"Here it comes, heads up," Toji said, dropping a large utility trailer with a giant spotlight on one end into the pit. Designed of visual air-search at night, or the same thing that civilians used to light up the night at the openings of big movies, it made a handy, EVA or Cherubim sized flashlight.

"Thanks," Aida said, catching the unit, and turning it into the darkness beyond. He could see the access way stretched out before him.

"I'm heading deeper into the structure."

There was the sound of shuffling, as he penetrated further, and several more scrapes and wrenches, as he tore open doors and squeezed through narrow passageways. Finally they heard him say, "Final shutter breached, now entering Central Dogma. Wow. Doctor Akagi, is this what Central Dogma looked like in Tokyo-3?"

"Very nearly, Aida. The Matsushiro facility was constructed using many of the same blueprints that NERV used for the Geo-Front facility," she offered.

"Wow, then I really missed out. This is incredible."

"Are the Magi intact?"

"Yeah, they look to be. The room is intact for the most part, there is some slight deformation to the ceiling, and I noticed on the way in here that all levels above this one have been crushed to form a protective bubble over the facility."

"Any signs of scavengers or anything else down there?" Doctor Akagi asked.

"Not really," Kensuke said, turning to examine the walls of the building with his light. "There's some odd damage on the walls, looks like energy blasts, probably from when Unit-03 was taken over."

"Negative, Aida. This facility was returned to pristine condition following the destruction of Unit-03."

"Well something made these marks," he said, running a hand over the hard surface, and feeling the deep scratches in the wall.

"Aida, I don't like this, I want you to withdraw slowly, and return to the surface. We'll perform a full subsurface scan before anyone else enters the facility."

"Okay Doctor Akagi, I... Hang on. I thought I saw something move."

"Kensuke, get out of there now," Toji was saying.

"I'm coming, I'm coming, hold your horses, this is a pretty tight fit through here you know. There, finally, I'm back in the main shaft, see?" he said.

Toji looked into the shaft, and could see Aida below, waving the light.

"I'm starting up now," he said.

"Phew. Kensuke old man, for a minute there you had me worried," Toji said, watching him climb the walls.

"No problems, it was probably just a trick of," he never finished.

"KENSUKE BEHINDYOU!" Toji shouted, as the light vanished, and a blur washed over Kensuke, blocking him from view.

###

Shinji and Asuka had just dried off after spending a leisurely afternoon alone within the shielded of his Jacuzzi when Shinji's Emergency Pager went off. They'd made love several times, and were both becoming more comfortable and daring each time, exploring and experiencing one another, as they adjusted to this new life. But something was intruding on their time alone, and Shinji felt a rising sense of dread, as he looked at the buzzing and vibrating device.

"Trouble," he said simply.

He ran to his cell phone, and picked it up, dialing Misato instantly.

"Shinji, Aida and Suzuhara have been attacked in Matsushiro. We don't know what it is. We lost contact with them almost as soon as Ritsuko called in the alert. Some kind of communications jamming. Just before we lost sensor contact we confirmed a Blue Pattern."

"Legionnaire," Shinji said, turning to look at Asuka. She gulped and looked grimly back at him, nodding in response to his unasked question.

"Sound the Alert, and clear the streets. We're coming," he said, hanging up the phone.

Shinji sprinted for the bedroom while Asuka grabbed at a suitcase that was sitting in the living room. Misato had brought several changes of cloths by and thoughtfully left them on the front door step, rather than disturbing them. She'd discovered them there the morning after she and Shinji had been re-united.

Shinji ran to his closet, stripping off his shorts, and pulled out a tight fitting pair of purple leather pants. He slipped into them as he ran down stairs, and opened the door to the closet, pulling out his matching jacket, boots, and motorcycle helmet.

Asuka goggled at the EVA in miniature that stood before her.

He reached into the closet and tossed her a leather jacket from within, and pulled out another helmet for her.

"We're taking the tubes?" she asked.

"Nope. I have something special that's been waiting for just such an emergency. Come on."

They ran out the door, and Shinji keyed the Garage door opener as he ran. The door slid open revealing a car covered by a large brown drop cloth.

"My BMW!" Asuka squealed.

"I saved it for you. I don't drive it, but I keep it running, and all the fluids are good. But that's not what we're here for," he said, stepping to the other side of the garage, and pointing to another shroud covered object, "This is." He yanked back the cover.

"Wow!" Asuka exclaimed, seeing the crimson and purple paint flashing in the dim light of the garage.

"When did you get this?"

"Kensuke gave it to me last week. Kind of an early birthday present. The old one was totaled, and we've spent the last three years looking for another one. They're pretty rare," he said, climbing on, and keying the ignition.

"How does she run?" Asuka asked, climbing on behind him.

"No idea. She's a Virgin. This is my first time with her," he said.

"Oh really?" she said slyly, "two in a week, Mister Ikari? You sly dog you."

Shinji flushed under his helmet. "I couldn't rider her. I needed something else."

"Oh? What was that?" Asuka asked, thinking the bike needed work before it was ready to run.

"My Riding Partner," he said, as he gunned the throttle, and the bike roared out of the garage, and into the street. Reflexively Asuka leaned into him and held on for dear life. She didn't even watch the gauges or the scenery as it flashed by, paying more attention to the subtle play of her lovers' muscles under his leathers.

'Yummy,' she thought as she felt his muscles bunch and flex beneath her.

"Phone. Dial Misato. Command." Shinji said, and this helmet comm. began to dial the base commander.

"Want me to open the tunnel Shinji?" she said, as she picked up.

"Um, yeah, how did you know?"

"Every camera on the base is tracking you. Aoba bet Hyuga you'd take the tunnels. Hyuga thought you'd take the 'Kiken' overland. They turned on every camera on the base to watch you come in."

Shinji laughed.

"Well open the tunnel and clear us all the way to the hangar, we're almost there," he said.

"Roger, tunnel open, you're good to go. Just don't break your neck on the ceiling when you drop in," she said.

"I'll slow down a little," he said and killed the comm.

"The tunnel?" Asuka asked.

"No. THE Tunnel. There's an emergency tunnel that leads from the park road ahead into the depths of the Base. The exit comes out in the Cherubim Hangar. There's twenty six ten meter thick hatches between us and them. At the speed we're traveling, if Misato doesn't open them ahead of us, we'll never stop in time. Although the AT fields would protect us, the bike would be a total loss."

"Heaven forbid," Asuka said.

Then the black maw of a tunnel was before them, yawning wide to accept. Shinji stomped the brakes, and chopped speed just enough to keep the bike on the ground as they crossed the threshold and began their steep decent into the base. Within moments they were streaking out of the tunnel, and into the Hangar. Shinji grabbed the brakes and slid the bike sideways, chopping speed. The bike came to a stop up against the far wall, and Shinji leapt off, as soon as Asuka had dismounted.

He took his helmet off, and looked up, his eyes widening in shock as he saw something he'd never believed he's see again.

A Red Evangelion stood next to his Purple one.

"Like it?" Asuka asked, throwing off her helmet.

"I love it. It looks like Unit-02."

"Same armor, different DNA," she said.

Shinji nodded, and started over to the front of his unit.

"Ready?"

"More than you'll ever know," she responded.

Twin AT fields reached for the EVA's and the two pilots vanished in a red glow.

"Unit-01 ready for launch," he sent to the Command Center.

"Unit-05 ready as well," came Asuka's voice.

He turned and looked at her, as she spoke.

"Hang on," he said, and the doors above them snapped open, and the two EVA's were launched towards the surface.

"Start to extend you're wings, when the catapult hits the surface it will throw us clear, and we can be airborne," Shinji said.

"Okay," she said, strain evident in her voice.

'She's only done this once before, but practice makes perfect,' he thought, thinking back to the time ten months ago when he learned to generate his wings.

Then they were shooting up out of the base, wings extended before them. With a graceful sweep, they gained altitude, and rose ever higher.

"Got co-ordinates for us Misato?" Shinji asked.

"Transmitting. We're getting some garbled signals from the area, but comm's are still down. Satellite surveillance shows that both Cherubs are inside the base, but the technicians have pulled back to their vehicles some 2 kilometers from the entrance. We're losing our visual capability though, storms are building over the Sea of Japan, and heading inland."

"Roger, We should be there in fifteen minutes," Shinji said.

He glanced over at Asuka in her red EVA, and an odd smile lit the face of his Unit-01. She turned her head to the side, and saw him, her EVA returning the oddly disturbing smile. She reached out and took his hand, and together they flew into the gathering storm.

Next: on Episode 3:02 of Neon Genesis Evangelion

Shinji and Asuka arrive at the Matsushiro base, and are dismayed to discover that there is no sight of Toji or Kensuke. Have their friends already fallen at the hands of a Legionnaire, or will Shinji and Asuka be in time to save them.

It's Evangelion Episode 3:02 The Terror Beneath