Disclaimer: I do not own Metal Gear, Metal Gear Solid or Metal Gear Rising. All rights belong to Hideo Kojima and Konami.

Tokyo, Japan, 11:50 AM...

John was being lead through the rain to an alleyway in Tokyo, to check the last sighting of his father, Raiden. He walked past the yellow tape as a Tokyo police officer lead him to the body, which was being covered by a tarp. He walked up to the body and kneeled down beside it before he lifted up the tarp just enough to see the face of the person that was murdered. And to John's shock and sorrow, it was Dr. Drago Pettrovich Madnar, the man that saved his father so many years before.

After his father's disappearance, the good doctor was a big part in John's life, teaching him all things science. He even helped develop John's cybernetic suit, a suit that resembles Gray Fox's cyborg body during the Shadow Moses Incident, helmet and all.

When John examined Dr. Madnars body, he noticed that were were multiple cuts all around his body, which indicates that his father had killed him. But why? Dr. Madnar saved his father twice in the past. Why would he kill him? John couldn't understand it, and it had already started to frustrate him.

John shook his head before he put the tarp back over the body. "Goodbye, old man. I'm sorry." He whispered softly before he stood up and walked over to the police officer that brought him here. "Do you know when the time of death might have been?" He asked the officer in Japanese. The officer then answered. "Our forensics team estimates that the possible time of death is within 24 hours." He answered. "24 hours? That's around the time that the base camp was attacked with Adam." John thought. "But... the timing seems too perfect. Way too perfect. I think there might be something more going on." He thought as he looked back at the tarp that covered Dr. Madnars deceased body.

He turned back around and looked at the officer again. "Thank you for bringing me here. Could you take me to the hotel please?" He asked him. The officer nodded and walked him back to the police car. John hopped in the back of the car and waited for the officer to start driving. "I have to get back to base and report this to Meryl. I hope Adam is doing alright with his first mission." He thought as the police car took him back to the hotel.

Seychelles Waters, Diamond Dogs Motherbase, 7:30 AM...

Phantom rowed the life raft to the bottom of the R and D Platform and found a ladder to climb up. He grabbed hold of the ladder and climbed up to find a way inside the platform to dispose of the Fenrir patrolling inside. As he climbed up, he found an emergency hatch to climp up inside the platform. He opened the hatch, climbed up inside and closed the hatch, however, unlike the Command Platform, the lights inside the R and D Platform were off, leaving Phantom inside of the platform, with the patrolling Fenrir, shrouded in darkness. "Remember, Phantom, when you encounter the Fenrir, aim for the head or it's chest to destroy it's power source. And aim carefully. The Fenrir Combat Unit was designed to be silent, fast and deadly. So, be careful." The voice reminded him over the radio.

Phantom nodded his head. "I remember. I'll do the best I can, so, for now, I'm going radio silent. I'll let you know when they've both been taken down." He whispered as he took out the Night Vision goggles and put them on his head. He readied his primary and walked slowly, and silently, down the narrow corridor of the platform.

It wasn't long until he heard the thudding footsteps of the first Fenrir that was patrolling the inside of the R and D platform near the first corner of the corridor. Phantom hugged the wall tight when he reached the corner, and took a big risk when he peeked his head from the corner to fully see what he was up against, and which direction it was going. Just like the security feed, the first Fenrir was indeed a huge canine looking machine and, thankfully, it looked to be heading in the other direction, opposite of Phantom. When it finished scanning the corridor, it turned and walked in the other direction, so, Phantom decided to try and take another risk by slowly walking up behind it to take it out quickly and silently.

But what would he take it out with? That was the question that currently lingered in his head. As Phantom continued to silently follow the unsuspecting Fenrir, he thought of countless scenarios in his head to figure out a way to take out the first Fenrir, but when each scenario turned out to be his death instead of the Fenrir's defeat, he made a split decision. "Aw, fuck it." He thought as he broke into a run and jumped on top of the Bio-Oraganic Machines back. The Fenrir, startled by the sudden increase of weight, began to jump and thrash around in the narrow corridor of the platform like a mad bull.

Phantom, holding on to the Fenrir tight while climbing up further on its back, managed to climb up to the machines head, readied his primary, and unloaded the entire magazine into the Fenrir's head, hoping to hit its power source. After Phantom emptied the magazine, the Fenrir stopped thrashing and just plopped down on the floor with a loud thud. Phantom then hopped off it's back unloaded the empty magazine and loaded another one into the assault rifle. He quickly made his way through the corridors of the platform to find a way outside. When he found a door leading outside, he removed the goggles and checked both his left then right to make sure he doesn't unintentionally run into the second Fenrir.

When he saw that the coast was clear, he walked outside slowly so he doesn't alert the Fenrir and lead it to his location. Just when he reached the first corner outside, he heard something growling behind him. He instantly stopped and slowly turned his head to the side to see the second Fenrir, standing ten or so feet away, staring right at him. The Fenrir's growling began to get louder and louder, before Phantom broke into a run away from the machine to get some distance. The Fenrir took off after him and chased him around the R and D Platform to catch him. Phantom didn't know the R and D Platforms corners all too well, but whenever he would see a quick turn to gain same distance away from the pursuing Fenrir, he would take that turn every chance he had.

While he was being chased in circles around the platform by the Fenrir, he readied the grenade launcher on his primary to use it as a way to finish off the machine quickly. After he made another turn away from the Fenrir, he readied his primary and quickly turned around to fire the grenade at the machine... but it wasn't there. Phantom checked the surroundings all around him to find the Bio-Oraganic Machine, but it was no where in sight. Until...

Thud... Thud... Thud...

"ABOVE ME!" He shouted at himself as he pointed his primary upwards to see the Fenrir jump down from one of the platforms buildings towards him.

He fired the grenade at the Fenrir, which exploded upon impact, and heard the machine roar loudly. The blast of the explosion sent Phantom flying into one of the platform buildings walls, before knocking him out. "Ugh..." He groaned as his vision blurred while he watched the roaring Fenrir thrash around in pain while trying to put out the fire.

Moments later...

"...antom... you ok... ple... swer me..." Phantom heard the voice on the radio calling out to him. He shook his head to shake away his grogginess before he attempted to stand up. "Phantom, are you alright? Please respond." He heard the voice again. When he felt well enough to reply, he answered. "Yeah, I'm fine. I was knocked out cold." He answered as he found the charred, burnt remains of the second Fenrir. There were still small flames surrounding it, but nothing too big to worry about. "Thank goodness. You didn't reply for twenty minutes after the explosion so I got worried." The voice admitted, making Phantom nod his head. "Yeah, sorry about that. The Fenrir almost got the jump on me. Literally." He sighed.

He then walked to the edge of the platform and sighed again when he felt the cool breeze brush against him. He stood like that for a moment before spoke again. "Alright, both the Fenrir's have been taken care of. Now, where are you?" He asked the voice. "Make you're way up the top of the platform. I'm in a hollow hole in the center building." The voice responded. Phantom looked confused, but he wasn't going to argue, so, he found the nearest stairway and walked his way up to the top.

When he reached the top of the center building and looked down into the hollow hole that the voice told him about, there was nothing there. Just an empty space with a large, cylinder shaped pod near the center of the hole. "Alright, I'm here, but... where are you?" He asked. The voice quickly responded.

"You're looking right at me, Phantom."

The voice answered, and as it answered, the red light on the pod blinked.

Phantom was shocked at this. Wanting to get closer, he climbed down the ladder into the hole, and walked up to the pod. "What are you?" He asked it. "I already told you, I am what's left of a memory that has been long forgotten in history. But, if you want a technical answer, I am an artificial intelligence created by a woman named Dr. Vanessa Strangelove. I was created by her to resurrect a personality of someone that had passed away. Someone she cared about, but I doubt those feelings were ever returned in kind." The AI pod answered.

"Then, whose personality did Strangelove try to resurrect?" Phantom asked. "You are not going to remember her name, let alone even know it, Phantom. She, like many others before her and after, has been erased from history. She was the greatest hero of the 20th century, but that will all be stories for another time. For now, I am happy to tell you that I will allow you and your comrades to make this base your new base of operations. Contact your superior, and tell them that this base is ready to be claimed, should they want it." The AI pod told him. Phantom smiled and nodded his head. "Believe me, my Commander wants this place badly. And she has every intention of moving Diamond Foxes here, whether she has your consent or not." He told the AI pod.

"The Diamond Foxes? Hmm, the rebirth of two memories. That's a calming thought. But regardless, you're all welcome here, and I can help you bring this base back to it's former glory. Whatever's left of that glory at least." The AI pod said to him. Phantom nodded his head. "Well, on behalf of all the Diamond Foxes, I thank you... uhhh... what should I call you?" He asked. The AI pod thought for a moment before it answered. "Hmm... well, I never had a name in the past, so, I don't know what you can call me really, but... if you like... you can call me The Boss." It responded.

Phantom tilted his head and smiled. "The Boss?" He asked. Then the AI made a sound, that sounded like a laugh, before answering. "I'll explain another time. For now, contact your superior and make your preparations." The "Boss" responded, making Phantom nod his head. "Alright, then. I'll contact my Commander and head back to base. Then we can start moving everything here." He said as he turned around to contact Meryl. "Wait, Phantom..." The Boss said. Phantom stopped and turned back around to look at the pod. "What is it?" He asked. "You wouldn't happen to know a Hal Emmerich, would you?" The AI asked. Phantom looked at the Boss confused. "You know Otacon? How?" He asked.

The Boss "sighed" before it answered. "Just... I'll tell that tale another time. Contact your superior and make your preparations." The Boss answered, making Phantom nod his head before contacting Meryl.

*Static*

"Phantom? What is it? Is everything alright?" Meryl asked as Phantom contacted her. He nodded his head. "Yeah, everything is fine, Commander. I ran into some... resistance, but it's been taken care of. Bring in a clean up team to get rid of the cluster. Also, I'm calling to report that the Seychelles Motherbase is bigger than we thought it would be." He answered. Meryl waiting a moment before responding. "Meaning... what?" She asked, making Phantom smile. "Meaning, that the Seychelles Motherbase has more than enough room to become the Diamond Foxes new motherbase." He answered.

Meryl was silent for a moment longer before she replied, though Phantom could already tell what she was about to do. "YES!!!" She shouted. Phantom chuckled.

"I'll send your helicopter back to pick you up, then we can continue things when you get back to base." She said before she ended the radio conversation. Phantom smiled and shook his head, before turning around to look at the AI pod. "Well, I'm going to be leaving soon. Are you... going to be ok here? Alone?" He asked the Boss. The AI laughed. "Phantom, I've been alone here for over 50 years. I think I'll be just fine for a few hours or days." It responded. Phantom nodded his head and contacted the pilot to pick him up at the R and D platform.

As he began to walk away, the AI called out to him one more time, making him stop. "Phantom... wait. I have a request." It said. He looked confused for a moment, but decided to find out what the request would be. "What is it?" He asked. The AI hesitated before speaking. "Hal, or as you know him, Otacon, will you be working with him?" It asked. Phantom was now even more confused about the AI's interest in Otacon. "Absolutely. Why?" He asked. The AI hesitated again. "When you come back here, will you... bring Hal back with you? To this platform?" It asked. Phantom paused for a moment before he nodded. "Well, he is a scientist, so, he's going to be working at this platform anyway. Along with his adopted daughter, but sure, I can bring him here. Why? What's your interest in him?" He asked again.

"Because I have something to tell him, and him alone. If he wants to tell you, then I'm sure he will when he's ready. But for now, what I want to tell him is for him. So, when you come back this base, will you bring him here to me? Please?" The Boss asked seriously, but there was also sorrow hidden behind it's tone. Phantom just stood there for a moment before nodding his head. "Alright, sure. I'll bring him to you. You have my word. I don't know when we'll get back here, so, just be patient." He answered politely.

The Boss answered again. "Phantom, being patient is what I'm good at. So, please, take your time, just remember to bring Hal to me when you make your way back here." It said. Phantom nodded before turning around to climb up the ladder and make his way to the helipad. As he neared the helipad, he could see the helicopter in the distance. "This is Echo-5, arriving shortly at LZ." He heard the pilot say on the radio.

It was only a few seconds later when Echo-5 arrived at the helipad. The sliding door opened and Phantom hopped in. Once he closed the sliding door, the helicopter rose higher into the air. "Gaining altitude." The pilot said as Phantom watched the AI pod and the, soon to be, Diamond Foxes Motherbase shrink in the distance.

The ride back to the current Diamond Foxes base gave Phantom some time to think about something. "The Fenrir Combat Unit was only patrolling the R and D Platform. Why? Because of the Boss? Or was it because of some other reason? Or both? Either way, this all seems to be too suspicious to drop and forget. There's something more going on. And we all need to be extra careful from here on out." He thought to himself.

"I need to report everything that happened to Meryl when I get back. Something fishy is going on, and we need to find out what." He thought as Echo-5 made it's way back to base.