This is literally the angstiest thing I've ever written and it made me sad. Also, this is a side story, but you don't need to read the rest of the series to understand what happens. Also also, fun fact: I haven't even started the actual series yet. Yaaay... The title comes from The Way from Xenoblade X.

I Will Wait For You: A Metal Gear But I Made it Gayer Side Story

The first time they slept together had been a mistake. Snake wasn't proud of that fact, but hey, he'd almost died. Cut him some slack. He'd come back, still bleeding, and Otacon was so cute and worried, that Snake couldn't help kissing him. Which led to really, really awkward sex, but Snake'd had worse.

(Otacon claimed that wasn't how it happened, and that he would never have sex with some one while they were bleeding, which caused Snake to ask about period sex, which caused Otacon to turn bright red. According to Otacon's version of events, while he was dealing with Snake's bleeding, Snake had kissed him. Snake couldn't really remember, because there was a slight chance that he'd been at least a little bit drunk.)

The next morning, Snake ended up having to wake up Otacon, who was sleeping curled in a ball, his face presses against Snake's side. The way he'd smiled sleepily and said, "Good morning!" was so goddamn cute that Snake was tempted to kiss him again. But he didn't. In fact, he'd done pretty much the complete opposite. He told Otacon that he didn't want to jeopordize their working relationship, and that last night had been a mistake (which was true) and that he wasn't at all attracted to him (which wasn't). Otacon had looked so sad, that Snake ended up caving just a little bit. What was the harm in becoming friends with benefits?

The second time they had sex was because Snake was bored. They'd gotten smowed in their shitty one-room apartment (which Otacon always insisted should be considered a two-room apartment because it had a bathroom. Snake was pretty sure that wasn't how it worked). Otacon was watching tv, or playing video games, Snake couldn't remember. So they had sex, after Snake checked with Otacon, of course. He wasn't a goddamn savage.

The first time Otacon told Snake he loved him was after the third time they had sex. They were laying in bed, Otacon tracing circles on Snake's chest.
"I love you," he'd said.
"Okay," was all Snake could think of to say.
"Okay?" Otacon echoed.
"What do you want me to say?" Snake asked, a bit too defensively.
Otacon rolled onto his side, facing away from Snake.
"I don't know," he said.
Snake wanted so badly to wrap his arms around Otacon's skinny body, to kiss his bony shoulder, his neck, but instead he said, "I don't love you."
It came out harsher then he'd intended, and he flinched.
"Oh," Otacon said, deflated.
He pulled his knees to his chest and sighed loudly.
"I-I mean, you're my friend," Snake said quickly, "And I-I love you as a friend, but... I'm not in love with you y'know."
"I'm sorry," Otacon said, pulling the blanket over his head, "I-I just thought- I'm sorry."
"It's fine," Snake said, placing a hand on the small of Otacon's back.

The next few weeks were incredibly awkward. And then Snake almost died again.

Something had gone wrong, though neither Snake nor Otacon was totally sure what. At the time, both of them had blamed themself, though at some point they ended up sharing the blame.

Basically, Snake had passed out, broken his leg, and sprained his wrist. He couldn't remember how he'd managed to do all that, which he chalked up to head trauma. Otacon had panicked and taken him to the hospital.

Snake had woken up in the hospital, Otacon in the chair next to him, reading. Snake must have made a noise, because Otacon looked up, startled, and dropped his book.
"David," he'd said. (Back then, Otacon had rarely used Snake's real name. Snake secretly loved it whenever he did).
Grunting, Snake tried to sit up, which was hard with one arm in a sling.
"Little help," he grunted.
"Oh," Otacon gasped.
He jumped up and grabbed Snake's good arm, putting his other hand on Snake's back to help Snake up. He stood there for a bit, absently tracing circles on Snake's arm.
"Hal," Snake said.
Otacon glanced down, and realized what he'd been doing. He quickly pulled his hand away.
"Um, sorry," he said.
Snake reached up and grabbed Otacon by the front of his shirt, pulling him down until their lips met. They kissed for a bit, until Otacon pulled away.
"We can't," he said.
"Can't what?" Snake asked.
Otacon stared at him.
"You know," he whispered, blushing furiously.
Snake started laughing.
"What?" Otacon demanded.
"That's not-" Snake laughed.
Otacon glared at him.
"Okay, are you still in love with me?" Snake asked.
"Uh, yeah."
"Good," Snake grinned, "'Cause I'm kinda in love with you too."
There had been a silence.
"What?" Otacon said finally.
Snake rolled his eyes, smiling.
"I'm in love with you, dumbass."
Otacon squinted at Snake.
"You said you weren't."
"I lied."
"Why would you do that?" Otacon questioned.
"We can talk about this later," Snake rolled his eyes.

They'd snuck out of the hospital, even though Otacon thought it was a bad idea (though he did eventually put his foot down when Snake had wanted to take his cast off himself).

Later had turned out to be when Snake and Otacon were in a hot-wired car (which Otacon felt bad about. He'd left twenty dollars in the person's mailbox, because apparently he genuinely thought that was how much cars cost.) driving to God only knew where (which turned out to be Minnesota).
"Why?" Otacon had asked, without taking his eyes off the road.
"Huh?" asked Snake, who was sitting with his broken leg propped up on the dashboard.
"You said we could talk later. It's later."
"Oh yeah. That."
"Why?" Otacon asked again.
Snake groaned.
"It's just... what if... this doesn't work out, y'know," he said, gesturing between himself and Otacon, "What happens then?"
"Nothing happens," Otacon said, taking Snake's hand, "We'll always be friends. Promise."
He squeezed Snake's hand and gave him a shy smile. Snake smiled back. He trusted Otacon, more then he'd ever trusted anyone in his life.

The fourth time they had sex was a month later. Snake had been laying on the couch, half paying attention to some documentary, while Otacon worked on his laptop.
"What're you working on?" Snake had asked, lazily running a hand through Otacon's hair.
"Makin' a sprite," Otacon had mumbled.
"What?"
"Here."
He handed Snake the laptop, the screen displaying a tiny, pixellated Otacon.
"Why?" Snake asked.
"'Cause it's cute," Otacon shrugged.
"Okay, but what's the point?" Snake asked, handing the laptop back.
"Mmm... not sure yet."
Snake laughed, "I thought you were doing work."
"I am!" Otacon insisted.
"Clearly, we have different deffinitions of work."
Otacon leaned his head back to look at Snake.
"'S cute," Snake grinned.
Otacon grinned back, and then loudly gasped. He shut the laptop and jumped to his feet, running into the bedroom.

He returned about a minute later, clutching a small, clumsily wrapped box. He went back to Snake and held out the box.
"H-happy anniversary," he said awkwardly.
"What?" Snake sat up and took the box.
"W-well it's been a m-month s-since we-we, um," Otacon explained, blushing furiously, "And, I-I thought..."
Snake opened the box. Inside was a necklace with a dog charm.
"I-I know you were s-sad you had to give away your d-dogs," Otacon explained. Then he shook his head, "I-I'm sorry, i-it's stupid."
"I love it," Snake announced.
Otacon's eyes widened, "Really?"
"Yeah," Snake grinned.
He slipped the necklace over his head and tucked it down the front of his shirt.
"I'm glad," Otacon said, relieved.
Snake pulled Otacon onto his lap. Otacon wrapped his arms around Snake's neck and pressed their foreheads together.
"I love you," he whispered, and it was the second time he'd said it.
"Love you too," Snake mumbled (the third time he'd said it, who would've thought), resting his hands on Otacon's hips.
And suddenly they were kissing, gently, lovingly, and Otacon's hands were in Snake's hair.

Afterward, they'd laid together on the couch, Otacon half on top of Snake (otherwise, he probably would've fallen off the couch, and Snake would have laughed at him), and Snake was struck by a strong desire to protect him. He silently promised Otacon that he'd never let anyone hurt him, and pressed a kiss to the top of his head. Otacon looked up at him so lovingly, that Snake kissed his forehead. Otacon hummed and pressed his face into Snake's neck.

By the time Sunny entered their lives, Snake had given up keeping track of the times they'd had sex, the kisses, the 'I love you's. He just didn't see the point anymore. He hadn't been able to keep his promise; Otacon had still gotten hurt; but Snake had done his best to take away the pain. For the first time in his life, Snake was truly happy.