The Secret War: Terrible Truth

Sequel to my first The Last of Us/Metal Gear crossover, we're now covering a new event, unlike the first story that only drew from the original Metal Gear, this one draws inspiration from Ground Zeroes and the Hospital Part of Phantom Pain, but the bulk of it will be from Peace Walker, anyway, enjoy.

Disclaimer: I don't own Metal Gear, The Last of Us or their characters.

Dark Openings

Two years had passed since the Outer Heaven Incident, in that time Yara and Lev had managed to integrate well with The Agency. But now things were problematic and they had gone missing after uncovering something important. Now, in a military encampment, late a night, under heavy rainfall and lit up only by lamps of search lights. There were soldiers dotted around on guard. In one section of the camp was a large prison camp with prisoners held in tiger cages, exposed to the elements. These prisoners were forced to wear dark yellow prison uniforms and were barefoot. Some were cuffed, with black cloth bags over their heads, others were not. All were miserable, one of them stood out, two years older than the last time she had been 'in the field' so to speak. The figure was female, a somewhat tall, lanky young woman, in her late teens, she had medium length black hair pulled back with dark brown eyes and tan skin. She also had a few notable scars on her face and was clad in the same dark yellow prisoner uniform as the others. It was Yara. She bit back a groan, covered in pain, the scars were just the visible wounds, there were others, under her uniform and then there was the mental and emotional pain, since she wasn't the only one who had been captured, but Lev had been caught too and had suffered far worse than her.

Unable to stop herself, she let out a soft sob.

'Lev, what...what could have...you, did they…?' She thought in dismay.

The worst part of all was that she had no idea where Lev even was, after some time being tortured together, they had been separated since and, hearing everything that was happening to her brother, Yara had pleaded with the man who seemed to be in charge, for a way to end things quickly, without there being any further chance of them possibly compromising the Agency. That was what led to this moment. She could only wait and pray. It was then she heard the footsteps and looked up. Standing before her cage was a tall man, broad shouldered and clad in all black. Pants, a shirt, long raincoat, gloves and shoes. He wore a fedora hat that shadowed the upper half of his face, only his pale skin could be seen through what little was shown of his face. He also had a notable scar down his face, coming out from under the shadows caused by his hat, down his cheek, just catching the left edge of his lip, coming down to the edge of his chin. The only other notable fact about this man was that his left arm seemed to be oddly stiff, not as mobile as his right.

He reached into his pocket to pull out a disc recording with a reader and gently tossed them into the cage.

"There." He said, his voice sharp and carrying a strong accent, as if from one of the Southern States of America. "It's done, as promised, quick and painless. Your turn comes at dawn. This is what happens when youngsters such as you play with fire."

With that Yara pushed herself along the floor of the cage, unable to stand due to her legs being broken as part of the torture. She picked up the disc and recorder and plugged in the earphones and listened, trembling. Meanwhile, the man turned and began to walk away. A small group of soldiers, dressed differently from the majority of those around the base, followed him through the camp. Some of the camp soldiers saluted to him as he passed, but he was unmoved and simply walked straight to the waiting helicopter. He turned to one of the soldiers.

"Status update." He demanded.

The soldier saluted and spoke. "Sir. As requested we've received the final components and finished assembly for Pupa, Cocoon and Chrysalis."

"Then we're ready for the next step, good, get on board." The man announced. "Next stop, Nicaragua."

They all boarded the chopper which then took off and began to fly away from the military base in Cuba.

At the same time as the chopper left, a figure was climbing up the cliff to the crest just north of the base. Reaching the top of the cliff and crouching on the bluff, the figure looked over the camp with narrowed eyes. It was Abby, also two years older, twenty years old with the same blonde hair, now greatly darkened by the rain, again in a fishtail braid, blue eyes and pale freckled skin. She had greater muscle mass than before, with a strong build now. She wasn't in her sneaking suit however, instead wearing dark jeans and a grey tank-top as well as black boots. But there was good reason for that. She reached up and touched just below her ear to activate her codec.

"Joel, I'm overlooking the base…" She said. "This is crazy, an American base on Cuban soil?"

Joel gave a short chuckle. "It's hard to explain, but it's basically a black site on the southernmost tip of Cuba. A little slice of American pie on Cuban soil, no legal jurisdictions and guarded by US Marines."

Abby sighed. "A perfect place to make...unwelcome people disappear. What do you think Yara and Lev found that led to them getting taken here?"

"No idea." Joel admitted. "But remember, due to the nature of this place, this is not an official mission. The Agency has not sanctioned this operation and your only extraction is by chopper, since Terry the pilot owes me a favour."

"I got it, no official equipment and if Terry gets shot down, it's over, we're trapped." Abby said calmly. "Otherwise usual rules, on-site procurement and stealth being the key."

"That's right, that's also why you don't have your sneaking suit or Vita-Meds. So be careful and try to keep casualties to a minimum, these guys are technically our allies after all."

"Got it, okay, ready to go."

With that Abby ended the call and stood up, ready to begin this unauthorized mission.

End of chapter, hope you enjoyed it, read and review please.