STORY: I'm all about alternative universes at the moment. This one asks the question: What would have happened if, when the whole crew was in the wall in the first movie, Trinity had rushed to the aid of Morpheus, rather than forcing Neo to leave him? Read to find out my opinion.

AUTHOR'S NOTES: This and chapter two were originally going to be a single chapter, but I decided against having a ten-page chapter when I realised that it would be a ten-page chapter. Like usual with my fanfictions, the story is already complete (meaning I've already written it) and I'm just uploading it chapter-by-chapter as I feel like it. I wrote this almost two years ago after I finished my first Matrix alternative universe, 'Deja Vu', but so far I've been too preoccupied with that to concern myself with this. Now that 'Deja Vu' is finished I can focus on other fanfiction (such as 'The Best Homework Excuse Ever', which will probably never get finished at this rate) and I can finally upload this. Personally I prefer 'Deja Vu' but I'll leave it up to you. I hope you enjoy 'In The Walls'.

Chapter one

The sound of footsteps and their own breathing were the only noises. The breathing was inside the wall, with the six of them. The footsteps were soft and precise – and in the bathroom.

Without warning two hands smashed through the wall and grasped Neo's throat. He dropped the gun he held to try and pry the locked fingers from his neck but the grip was iron.

"It's an agent!" Cypher called from below. Those words made Neo panic further. An agent had him, and was going to kill him! No one else seemed to know what to do about it. Except for Morpheus, their leader. With an empowering cry of rage, he slammed himself through the wall and onto the agent that had Neo on the verge on unconsciousness. The hands fell away, and Neo's breathing and vision came back. But now Morpheus was in the grungy bathroom, pinning the agent down with his weight and nothing else. That knowledge did nothing to calm Neo's internal panic.

"Morpheus!" Trinity screamed, her voice anguished. Only a few metres below Neo, she had seen and heard what had happened. She started scrambling up, horrified. Neo had never seen her horrified before. She always had control over herself. She looked like she was about to stop, but Morpheus yelled back to her, "You must get Neo out! He's all that matters!"

He still thought that Neo was the One! He was going to sacrifice himself, like the Oracle had said!

"No, Morpheus! Don't!" he shouted, climbing higher. Trinity was faster – she was already at his ankle, and ascending. She didn't seem to care if she slipped.

"Trinity, go!" Morpheus ordered loudly, looking back over his shoulder. Neo looked down at her, but she didn't meet his eyes. She clambered up beside him, clinging to the handhold she found as she leaned back.

"Go!" she yelled, but didn't go herself. The others let go of their handholds and let themselves noisily fall to the basement, seven storeys below. There was a crash as Apoc, Switch and Cypher landed at the bottom.

"We can't leave him," Neo said forcefully as Trinity reached his chest-level. She looked up at him with her clear blue eyes and reached for the next safe handhold. She missed. Her eyes widened as she started to fall, but Neo snapped out his hand and caught her by the elbow, pulling her upright. She pulled herself higher and started to climb past him and out the hole in the wall caused by Morpheus. He grabbed her wrist and looked at her, not knowing what she was doing but needing her to understand.

"We can't leave without him," he said again. Trinity yanked her hand free and landed on the bathroom floor.

"I'm not going to," she answered, turning to the two men on the floor. Already, the agent – the same agent that had put that bug into Neo's stomach – was throwing Morpheus off. Without waiting for anyone to acknowledge her presence, Trinity leaped into the air and almost seemed to pause there, displacing time for the tiniest of moments, before kicking the agent in the head. The man took a step back, and she landed, already punching her opponent in the nose.

Morpheus got to his feet and watched sorrowfully as Trinity failed to dodge a heavy punch. She blinked as the fist connected bodily with her jaw, once, twice, thrice, four times. The agent's hand was closed over her throat, but she was past caring.

Neo came to his senses and jumped through the hole in the wall. He landed beside Morpheus. He couldn't watch this.

Even though the captain tried to stop him, Neo strode forward angrily. But by the time he had grabbed the agent's shoulder and yanked him back, the 'man' had already thrown Trinity into the small crowd of waiting men. They clamped handcuffs around her wrists before she could fight back.

Neo literally smashed his fist into the face of the agent, stunning him for a moment. That moment was all Morpheus needed. He leaned forward, grabbed Neo and threw himself at the wall, breaking a huger hole than even before. Then he got inside the wall, between the layers, and let go, dragging Neo behind.

Neo landed on the basement floor, eight storeys below. A large group of guards were trying to get into a trapdoor nearby, and smoke and dust reigned the air. Upon hearing them land, they all turned, but Morpheus had a gun out instantly and was shooting them down. Neo started to stand, and his hand brushed the gun he had dropped earlier. He snatched it up but it was out of bullets. Suddenly bullets started firing from between the slits in the ventilated trapdoor, taking down the enemy snipers.

Within a few seconds, most men were down, and the ones that remained standing were far away from the trapdoor. Neo darted forward and it was pushed aside by someone below. He dropped down and landed amongst the remaining crew. Morpheus joined them a moment later and they all bolted as soon as Switch had replaced the trapdoor. Almost three minutes passed where nothing was done but running before Apoc announced that it was safe to stop and find their direction.

Neo rounded on Morpheus in a fury.

"Why did you drag me away?" he demanded. Even in the almost darkness, Morpheus looked surprised by his reaction. No one else spoke as Neo continued. "How could you leave her there? They could kill her! The two of us together could have taken out the agent. Why did you leave her?"

"Neo, I understand your concern, but-" the captain began, but Neo got even angrier.

"Concern? I'm a little more than concerned. Tell me, what's the best-case scenario for Trinity right now? Death sentence? Life imprisonment?"

"What the hell happened?" Switch asked, trying to break it up. Neo turned to her, and, amazingly, she took a step back. Switch wasn't afraid of anything.

"Morpheus left Trinity there," he told her tensely. She paled, and Neo wondered if she was going to faint. She was so pale naturally – she was like a ghost now. But she didn't question Morpheus's judgement.

"Was there no other way?" Apoc asked hesitantly. He seemed a little shaken by this news – already today, Mouse, the youngest member of their crew, had been killed.

"I'm sure there was," Neo said angrily, facing Morpheus once again. The captain sighed sadly.

"Neo, will you take one moment to listen?" he asked. No answer. "Under any other circumstances I would have stayed and fought for her life, Neo, just as you wanted me to. Had there not been an agent, I would have. Had your life not been at stake, I would have."

"Morpheus!" Neo exclaimed, frustrated. "My life? Who cares about my life? What use am I? I can't do half as much as she can! If this about who you need for your damn ship-"

"No, this about the survival of the Resistance," Morpheus said, holding onto his patience. "You are the One, Neo, and-"

"I am not the One!" Neo shouted. "I'm not. I'm just some guy, okay? I'm just Neo, and nothing more than that. Christ, I should have told you the second I knew. But you told me not to, so I kept it to myself."

There was a ringing silence, where Neo's terrible words echoed endlessly in the dark tunnel.

"You are," Morpheus said finally.

"I'm not! Your Oracle told me so. There. You know. So don't tell me I'm more important than Trinity, okay? I'm not."

Everyone absorbed this news.

"You think I'm a horrible person," Morpheus said softly. "You think I wanted to leave my second-in-command at the mercy of the system. You think I don't care about her." He met Neo's eyes, and the newcomer felt some of his anger turn to guilt. "You mistakenly think that are the only person who cares at all for Trinity. I have known her too long to willingly give her for anyone."

"Then why did you?" Neo asked, his furious anger more irritation and worry now.

"Because I had to," the captain explained. "If she had just gone ahead with the rest of you, everything would have worked out fine. I only wish she wasn't so stubborn sometimes."

"She wasn't being stubborn, she was acting in loyalty," Neo said moodily. He looked down, upset. He wanted her back. Of everyone in the crew, she was the one he had bonded with. There wasn't anyone else in the real world that he could relate to like he could to her. "What will they do to her?"

"Are they going to kill her?" Switch demanded, nervously. Apoc and Cypher looked to Morpheus in interest and hope that he would shake his head or something.

But the captain hesitated. He thought for a moment, then said, "Undoubtedly, but not immediately. There will be legal issues to overcome, court cases… The justice system of the people will take time, but the agents will be quick to 'question' her. They know that we won't leave her alive long enough to go through with proper sentencing."

"What are you talking about? We can't kill her," Neo said, shocked. The others glanced at each other solemnly.

"Sometimes it's more humane," Apoc said carefully.

"Like with pets," Cypher agreed, but he looked terrible. "If your cat or dog is in incurable pain, the vets suggest putting them down. It's like that."

"Trinity is not a cat or a dog," Switch said in almost perfect unison with Neo. She sighed. "But he's right. If the agents don't, some sick federal bastard will torture her. And it won't be physical torture. They torment the mind with some drug."

Talking about it seemed to scare her.

"There has to be something we can do," Neo insisted. No one answered him. "Something I can do, if none of you will help me."

"Neo, be reasonable," Morpheus tried. "She'll be under heavy guard all the way to wherever they hold her, and that'll be a top security cell. Let's at least go back to the ship so we can watch her progress. Come on, we'll see if we can't work something out," he added gently.

So Neo miserably followed the others, not saying a word as they made a path through the tunnels and finally came up in the centre of a road, in a manhole. Morpheus led the other four down the road and along winding streets, taking directions from Tank, the operator. They finally arrived at the old television repairs shop to find the ringing phone, which was in fact their exit from this world.

Switch gratefully took it into her hand and held it to her ear like she was answering a call. Her image dissolved into fragments and she seemed to disappear into the phone line. The receiver fell to the floor, and Cypher replaced it to its cradle.

Neo said nothing until it was his turn. He looked at Morpheus as he hung the phone up from Cypher leaving.

"I know you're lying to me to get me out of the Matrix," he said quietly. The captain seemed surprised.

"I'm not lying, Neo. I want Trinity back, too. We just need time to think of something to do."

"It doesn't matter," Neo said. "I just want you to know this: I won't be able to rest until we have her back."

"I know, Neo."

"I can't stand the thought that we – I – can do absolutely nothing to help her," Neo added hesitantly. Morpheus merely nodded. The exit rang. Neo answered it like the others had.

The next thing he knew, he felt the alien sensation of being pulled back as a separate thing to his body. He opened his eyes in the gloomy confines of the Nebuchadnezzar, half-expecting to see Trinity standing above him like she usually was. Hoping to see her hang the plug up behind his head in its place and tell him how well he did in that training simulation like she usually did.

But she wasn't there. He sat up while Dozer hung up the plug and looked around, dying to see her walk in with a rare smile, or even her usual neutral expression.

But he saw her lying still in her chair, still plugged into the Matrix beside him. Her regular, shallow breathing was soft and inaudible, and her chest rose and fell gently like one in a restful sleep. Her expression of utter peacefulness, her relaxed, limp form, and her closed eyes belied the horror she must be going through.

Neo stood and stepped up to her. He laid one hand on hers as she had the first time the cranium plug had been inserted into his head outlet.

"Go and eat, everyone," Morpheus said tiredly. "I'll try to think of something."

Murmuring, the others moved off, headed for the eating hall. But Neo remained with the captain and the two Zion-born brothers, Tank and Dozer. And Trinity, too.