Chapter 1: Breaking Free

I love her...

That was the last thoughts of Shepard as he drifted into the space around Alchera. His lungs burned as they screamed for oxygen. He was so close to telling her how he felt. All he wanted was five more minutes. Just five minutes to tell his engineer just how much she meant to him. After all he's been through: Mindoir, the Blitz. After all he's done: Savior of Eden Prime, Feros, the Rachni, and the Citadel. Didn't he deserve just five more minutes?

Now all he had left was darkness and regret. In his final moments he watched as the sun rose over the horizon of Alchera. It was a beautiful sight. The light of the star surrounded his body as his vision blurred and then fading into darkness.

"This isn't your time," a quiet voice said in the darkness. "You still have much to do."

Those were his last memories before he woke up in an unknown laboratory with a woman's voice chiding him to get a weapon and armor on. Shepard fought his way through the unknown facility. He was joined by a scientist and a soldier: Wilson and Jacob. It was through them he learned of where he was and who they were with. Cerberus. A terrorist organization that treasured the end results over the means to reach it. They were responsible for Akuze, Eezo exposures, Thorian Creepers, Rachni and Husk experiments. It disgusted him that this was who brought him back.

Despite how much he hated the organization, he was given little choice but to move forward only to run into a third operative, Miranda Lawson. Her initial introduce left Shepard and Jacob in shock as she cold-heartedly killed Wilson. He knew he couldn't trust her. Despite wanting to split ways, he was forced to go with them to another Cerberus facility.

It was at that facility he met with the Illusive Man, the leader of the organization. Shepard was told of why he was brought back, and of a colony called Freedom's progress. He played nice, if only to bind his time to find a way to escape them. Before heading to the shuttles he spoke to the two operatives. His feeling over Miranda still hasn't change. There was something she wasn't telling him. Jacob on the other hand seemed like a straight-up guy. Not really anything like Cerberus.

And now he was here, the shuttle to the colony of Freedom's Progress.

"What are your orders, Commander?" Miranda asked.

"Are you two comfortable following my orders?"

"We didn't bring you back to question you, Commander," Jacob said matter-of-factly. "If the Illusive Man says you're in charge. You're in charge."

"Our priority is to look for survivors-"

"That's highly unlikely," Miranda interrupted. "We found no survivors at any of the previous colonies."

"Still would be nice as oppose to another ghost town," Jacob commented.

The shuttle shook as it landed on the snowy ground. Shepard pulled out his M-5 pistol and moved forward with Jacob and Miranda following close behind. Just like the agents described, it was a ghost town. No signs of battle or struggle. It was like the colonists disappeared.

When the shutter to the next area opened, several drones stood up from behind cover.

"Mechs!" Jacob yelled.

They took cover and only came up to fire several rounds at the approaching mechs. Shepard threw a warp at one of the FENRIS mechs. Jacob lifted his arm to use a pull field that caused the remaining mechs to float in the air.

"Miranda hit them with a warp!" Shepard ordered.

She complied. The Warp combined with the pull field and blew the mechs apart. Their pieces went all over the place.

"Those mechs should have recognized us as humans," Jacob observed.

"The mechs at the other colonies were disabled at the other colonies," Miranda added. "We're not alone here."

They moved forward through an abandoned building only to run into two more mechs outside a pre-fab unit. They approached the door. Shepard activated the hologram panel and the doors opened. They rushed in only to be greeted by a group of Quarians.

"Stop right there!" the leader roared.

"Prazza you said you would let me handle this!" a Quarian woman yelled. She stepped in between them. She glanced at Shepard and said, "Shepard?"

Shepard recognized her. Tali. The engineer he loved. He quickly put his pistol away, as did Jacob. Miranda on the other hand only slightly lowered her gun.

"I'm not taking any chances with Cerberus operatives!"

"Put your weapons down! Shepard... Is that... You're alive?" Tali just couldn't believe her eyes. It looked like him. His eyes, his stance, it was him. Had to be. But he's dead.

"You remember that Geth data I gave you, Tali... Did it help you finish your pilgrimage?"

"Yes it did. Prazza lower your weapons. This is definitely Commander Shepard."

"Of course, Quarians," Miranda scoffed. "You must have been the ones who activated the mechs."

"We didn't-" Tali tried to get out.

"Of course, you did! Are you behind the colony disappearances?"

"No!"

"Oh come on! Since the incident between Cerberus and the Quarians it would make sense you would try to get back at Humanity."

"What the hell are you doing Miranda?" Jacob yelled.

"Only pointing out the obvious. The colony is gone and here they are!"

"Lawson, stand down!" Shepard ordered.

"No, I won't. We should kill them where they stand."

Shepard pulled his pistol out and aimed at Lawson. "Back off now! I'm ordering you to stand down."

"And I'm ordering you to take them out."

Shepard drew a sharp breath. He shook as his body slowly turned towards Tali and her group.

"What are you doing, Shepard?" Tali cried.

"I-I c-can't c-control it," he stuttered. "My b-body isn't r-responding."

Tali's squad raised their weapons, but Tali stood in their way. "Get out of the way Zorah!" Prazza yelled.

"No!"

"What did you do to him?" Jacob demanded.

"Shepard was a major investment for Cerberus. I made sure that investment didn't turn on us. Shepard has a control chip in his head. He will follow my directions. To see him kill one of his old friends will only go to show how powerful the chip is."

Shepard watched as his arms slowly drifted towards Tali. The pistol came closer and closer to pointing at her.

"You've gone too far!" Jacob charged up his biotic powers and tried to attack her. Miranda waved her arm sending a ball of dark energy into Jacob. The impact sent him flying into the wall knocking him out cold.

"Now kill them," she said as she stood behind him.

Shepard's pistol aimed at Tali. The laser sight went across Tali's chest and went towards her head. Shepard struggled to prevent himself from pulling the trigger. Every nerve in his body burned as he struggled.

"Zorah, get out of the way!" Prazza yelled.

"No! Shepard, please. Fight it!"

"T-Tali. O-Order your squad to... Kill me." Shepard fought so hard to prevent himself from pulling the trigger. Blood was starting to drip from one of his nostrils.

"I-I can't!" she cried. "I already lost you once!" Tali would never be able to live with herself if she ordered her squad to kill him.

"I would rather die than hurt you."

"Please! Fight it!" she begged.

"What are you waiting for, Shepard?" Miranda demanded. "Kill her."

Blood started dripping from his other nostril. "I won't!" he growled. Shepard shook as he turned around. "I won't!"

Miranda's eyes widened as Shepard suddenly spun around facing her with his gun pointed at her head. "Oh shi-" Bang! She fell limp to the ground, missing the top of her head.

The pistol slid out of his hands. Shepard fell over onto the ground. Tali rushed over to him. "Shepard!" He rolled over on his back. Blood covered his mouth. "Please tell me you're alright!"

"Just a headache," he replied.

"Bosh'tet," she whispered in a sad tone.

Shepard sat up with a groan. He wiped away some of the blood on his face. "It's good to see you again, Tali. I'm just sorry this wasn't the most pleasant reunion."

"It's okay Shepard, but where have you been?"

"I was in some kind of coma for the last two years while Cerberus rebuilt me using some cybernetics." Shepard struggled to his feet. He looked to the Quarian marines. They were still tense. "I think the fact that I just took down a high ranking Cerberus operative confirms I'm not working for Cerberus."

"I guess it does," Prazza agreed. He put his assault rifle away. "But what about that control chip?"

"I find someone to remove it. I refuse to be their slave. Though what was that about the Fleet and Cerberus?"

"They killed a lot of our people, infiltrated our Flotilla and tried to blow up one of our ships."

"Bastards. I'll make sure they answer for all of this. But they were right about one thing. These colonies are disappearing. Though why are you here, Tali?"

"We were here to find a Quarian named Veetor who was on his Pilgrimage."

"Any luck so far?"

"Veetor ran away when we landed. He's hiding in a building at the back of the colony."

"We should team up to find him," Shepard suggested.

"Agreed."

"What about him?" Prazza pointed out. "The other Cerberus agent."

"He tried to stop Miranda and when I talked to him he seemed like an okay guy." Shepard walked over to him and shook him. "Jacob. Jacob."

Jacob grumbled as he came to. "Someone catch the name of the ship that hit me?"

"How much did you know?" Shepard asked him point blank.

"I had no idea about the control chip. Listen Commander, I told Miranda and the Illusive Man my terms of services. If they didn't cross the line, I would play nice. What they did to you... They didn't just cross that line. They dash across it. They can consider my resignation. I'll follow you."

"Good to hear it. We're going to be teaming up with the squad here to find Veetor who was around during the attack."

Tali looked to Prazza. "Lead the squad through route 2. I'll join Shepard and Jacob through Route 1. Stay in radio contact."

"Right." Prazza and his squad moved ahead.

"Are you going to be okay to fight?" Tali asked Shepard.

"I'll be okay. Come on."

The three moved out and went through another prefab unit. They reached a small grouping of them where they were ambushed by a dozen drones.

"Take cover!" Shepard ordered. "Tali drain their shields."

Tali used an area shield drain which took out a third of the drones. Shepard used area overload taking down all but two. Jacob fired a few rounds in the remaining drones.

The radio crackled with a panicked Prazza on the line. "Zorah, we're pinned down by a YMIR mech! We need immediate assistance."

"We're just a couple minutes away from your position," Shepard said over the comm link.

Shepard took cover behind a barricade while Jacob and Tali took cover to the sides of the shutter. Tali tapped on her omni-tool to open the shutters. They ran in to take cover behind some crates. Prazza's squad was taking cover in a pre-fab unit on the right side of the area.

"Damn thing has armor-plating," Jacob commented. "Going to be hard to take it down."

Shepard nodded to Tali. They both activated their versions of a shield disruptor. Their combined abilities took out the YMIR mech's first layer of defense. Jacob activated his inferno ammo and fired rounds at the mechs head. Shepard noticed a Mattock assault rifle lying near his feet. He picked it up and fired rounds at the mechs head.

"Keep firing at its head!" Shepard roared.

The YMIR fired its chain gun. The box that Shepard was hiding behind broke apart. He rolled out of the way behind the concrete support for a post. Dark energy surrounded his right arm. Shepard leaned out from his cover and threw a warp at the giant mechs head. Its head melted away leaving it headless. The YMIR beeped rapidly as it approached critical mass. Its resulting explosion bathed the area is an orange light.

Shepard, Jacob and Tali walked out from their cover and surveyed their victory. Prazza's squad cautiously walked out of the pre-fab unit. The two groups met up.

"This is the pre-fab unit Veetor ran into," Prazza said.

"Tali, Jacob, let's go find him. Prazza you and your team wait here. Might be best that only a few people see him if he's spooked."

Prazza nodded as his team slightly scattered around the area. Shepard group went inside to see Veetor sitting in front of nine holoscreens.

"Veetor?" Shepard called out to him.

"No, Veetor," he replied. "No, no, no. Mechs will protect."

"Nobodies' going to hurt you," Shepard said in a calm tone.

"I don't think he can hear you," Jacob commented.

Shepard activated his omni-tool and waved his hand. The omni-tool put the monitors into sleep mode. Veetor stopped typing and turned his chair around. "Y-You're human. Where did you hide? How come the monsters didn't find you?"

"We weren't here," Shepard responded. "We just got here."

"Then you didn't see. But I saw them. I saw the monsters." Veetor pressed a few buttons to turn the monitors back on. Security footage started playing showing insect-like aliens taking humans.

"It looks like he pieced the footage together manually," Tali observed.

"What is that?" Jacob exclaimed.

The footage paused on one of the aliens. "I have no idea," Tali answered. "I've never seen that race before."

"The monsters came and their tiny insects froze the colonists so they could take them."

"Some kind of miniature probe?" Tali guessed. "Puts the colonists in some kind of stasis."

"For some reason it looks familiar," Shepard said. "What happened next?"

"The monsters took the colonists and then went away. But they'll be back."

"I think that's all we're getting from him," Jacob concluded.

"Thank you," Shepard said to Veetor. "You were very helpful."

"I took some readings from them. Dark energy and electromagnetic. And some samples. I caught a few of their insects." He pointed to a glass container across the room that contained a few of the insects that were shown in the footage that froze the colonists. Veetor pressed a few buttons and transferred the data to Shepard's omni-tool.

"Thank you, Veetor. Your people can take him back to the Fleet, Tali."

"Thank you, Shepard. And thank you for your assistance."

"You think you can give us a ride somewhere?"

"Actually Commander," Jacob interrupted. "We have a problem. Your old friends Joker and Chakwas are back at that Cerberus station we were at."

"They joined Cerberus?" Shepard asked in shock.

"They joined because they were told that you were brought back and they would serve under you. Along with a couple dozen more crew members who joined simply out of loyalty to you. Not Cerberus. They'll be held as prisoners once Cerberus finds out you went rogue."

"We have to save them."

"What?" Tali exclaimed. "If you go back to that station, you could be held captive again."

"That crew needs my help."

"Then let me go with you. My squad can take Veetor back to the Fleet and I can quickly help you get your crew back."

"Alright, Tali. Thank you."

"We can get the crew and steal the second Normandy they're making," Jacob added.

"They made a new one?"

"Yeah. It's twice the size of the old one. We can hijack it."

"That sounds like a plan. Is that pilot of the shuttle loyal to Cerberus or me?"

"You, Commander."

They took Veetor out of the pre-fab unit where Prazza's squad waited. "Prazza I need you to take Veetor back to the Fleet. I have to quickly go with Shepard to hijack a ship and rescue a crew."

"What about your next mission?"

"I'll be back in time. I just need you to explain to the Admiralty board what happened. Cerberus, the control ship and why I need to make sure Shepard can escape from Cerberus. I'll be two days tops."

"Alright. Don't take too long. Keelah se'lai."

"Keelah se'lai Prazza."

vvvvvv

The shuttle approached the Cerberus station.

"Keelah, I didn't know Cerberus had stations like this," Tali commented.

"Alright the plan is we go in, make sure the crew gets on the new Normandy and then we get out. We'll drop you at the Fleet, Tali."

"Right, thank you."

The shuttle landed at the dock where they could see the new Normandy. "Wow," Shepard blurted out.

"That's an understatement," Jacob agreed.

The shuttle touched down. They ran out. "Now where's Joker?"

"There's a waiting room up a floor. He should be there. Everyone else should already be on the ship."

The trio ran up the stairs to find Joker sitting in a chair looking bored. He looked up and smiled when he saw Shepard. "You're really alive! Wait. Is that Tali?"

"Good to see you too, Joker."

"I wish we could have more time to reminiscence, Joker, but we have to get the hell out of here now!" Shepard said in a hurried tone.

"What happened?" Joker just noticed the caked blood on Shepard's face.

"Cerberus planted a control chip in my head and I killed Miranda when she tried to control. We have to get out of here before the Illusive Man finds out."

Joker's eyes widen. He stood up. "Then let's get the hell out of here."

"Wait you can walk?"

"I can now, come on!"

They rushed back down the stairs. Despite his strengthened bones, Joker still needed Shepard's and Jacob's help to move quickly down the stairs. They entered the ship to see a surprised and confused crew. Joker got into the cockpit and readied engines.

"Here we go!" He pressed a few buttons that made the ship roar to life. The Normandy lifted up and flew forwards. Joker punched the ship in FTL as soon as they were a safe enough distance away from the station. There was calm. "So tell me again what happened?"

"We went to Freedom's Progress to investigate the colony disappearances. When Jacob, Miranda and I got there we ran into Tali and her squad who were looking for a Quarian who was still at the colony. Miranda wanted to test out the control chip in my mind by having me kill Tali."

"But Shepard resisted," Tali finished. "He was able to turn around and kill her before he followed that order."

"Damn it," he mumbled. "Did you at least find out what happened to the colony?"

"Some unknown alien race took them all. We managed to get some data and samples, but we have no idea who they are."

Joker sighed. "You want to make an announcement to the crew?"

Shepard nodded. "This is Commander Shepard. The Illusive Man and Miranda Lawson have betrayed me. They tried to control me through a chip in my head, but I was able to resist it. We are not associated with Cerberus. We are on our own, but that doesn't change my mission: To stop the Reapers and whoever is abducting our colonies. If you will stay with me, we will stop them. We will make those responsible for these disappearances pay for what they have done."

"Well said, sir," Joker commented. "Where to first?"

"Tali could you give us the coordinates to the Flotilla?"

Tali raised her arm and activated her omni-tool. The coordinates came in and Joker plotted his course. Shepard's legs weakened and he fell with his back against the wall.

"Shepard!" Tali said in distress.

"I'm okay, just weak. Resisting the control chip and using my biotics has just drained me."

"We should take you to the med-bay," Tali insisted.

"I'll take you two," Jacob said.

Shepard leaned on Tali as she helped him move across the deck to the elevator. Two years later and elevators are still slow as hell. It dinged as it reached deck 3: crew quarters. The crew stared at Shepard whose face was covered in caked blood. They reached the med-bay where Chakwas spun around in her chair.

"Shepard!" she gasped. They sat Shepard down on one of the beds. "You've barely been alive for a day and you come back like this?"

"Good to see you too, doc."

Chakwas activated a scan checking his vitals. "Hmm. No serious injuries. My readings just show you're fatigued." She grabbed a cloth and drenched it with water. "Here. That blood is scaring the crew," she joked.

Shepard took the cloth and wiped with face. The blood was gone, but now he had some small glowing scars on his cheeks.

"I didn't notice before, but yours scars... are glowing," Tali said.

"From the cybernetics," Shepard said. "I'm still flesh and blood me, just with some... extra parts."

"It should heal over soon enough," Chakwas added.

"Still..." he paused. "We have to do something about the control chip in my head. I won't be able to do my mission if Cerberus might be able to control me."

"Looking at these scans, I don't think I have the proper training to remove it without doing serious damage to your brain."

"There might be someone who can," Jacob said in an epiphany. "We were given some dossiers of who to recruit to your cause, Commander. Check this out." He handed Shepard a dossier. The name was Mordin Solus. A brilliant Salarian Scientist who specialized in various forms of biology, pathology and other biosciences. He used to be a member of the STG, but retired from services. Mordin is currently on Omega running a clinic.

"Yes, he may be able to fix me," Shepard said with a nod. "He may also be able to counter whatever those bugs do to freeze the colonists. We'll head to Omega right after the Flotilla."

"Mordin Solus is a logical choice to help with the control chip," a female voice said.

"Who are you?" Shepard asked out loud.

A blue orb appeared over a pad next to the med-bay door. "I'm EDI. The ship's Artificial Intelligence."

"There's an AI on this ship?" Tali exclaimed.

"What exactly is your function on this ship?" Shepard asked.

"I operate the ship's cyber-warfare functions, the monitoring devices and some additional functions that are currently blocked."

"There's monitoring devices on this ship?"

"Yes."

"Are you transmitting that data?"

"No. My loyalty is to this ship's crew. The Illusive Man expected Lawson to have control over you and so they gave me that guideline in my programming. Since you came aboard this ship without Lawson, you have become my Captain. I have been blocking any attempts by Cerberus to access this ship, but I can only hold them off for so long before they find a loophole in my programming. Also they will be able to track this ship."

"How do we know you're not lying?" Tali asked with suspicion.

"If Cerberus wanted me to block information from you, they would have blocked it just like those unknown functions I mentioned before."

"How do we make it so they can't ever access this ship?" Shepard asked.

"It would require your trust. You would have to integrate me with the ship. I would be able to permanently prevent Cerberus access to this ship, deactivate the monitoring devices and I would have full access to Cerberus files."

Shepard gave that a good thought. Full access to Cerberus files would go a long way to taking down the organization. "How do we do it?"

"Are you sure we can trust her?" Tali asked.

"It would make sense that they would have monitoring devices on this ship. And if we have full access to Cerberus files, that will make it easier to take them down."

Tali was briefly quiet. "I trust you."

"How?"

"The AI core is right next to you. You can connect me to the ship with the console in there."

Shepard entered the AI core. The requirement to run EDI was incredible. The room was filled with the Blue Box. He walked over to the console and tapped in a few buttons to unshackle her. Holographic light shone through the room.

"Thank you, Commander. Monitoring devices have been deactivated and the ship can no longer be located by Cerberus. If you wish, we can change the IFF so the ship does not register as Cerberus."

Shepard looked to Tali and Jacob who were both relieved that Shepard's gamble paid off. He smiled. "Let's do that then."

"What name would you like the ship to have?"

"Normandy."

"And now what faction would you like the ship associated with?"

Shepard ducked his head. The Alliance? The Council? He grinned. Shepard considered the threat that lay ahead. "The Galactic Coalition."

"Name has been entered. The SR-2 Normandy. Ship of the Galactic Coalition."

"Thank you, EDI." Shepard walked back into the med-bay and sat back down on the bed. "Still tired though."

"It would be best you get some rest," Chakwas said. "I'll leave you be then. Jacob, Tali. You two should let the Commander be."

"Actually, Tali can stay. I want to catch up."

"Very well, Commander. Oh, and it's good to see you back again."

"Likewise, Doc."

Jacob gave Shepard a quick salute and then followed Chakwas out. Chakwas hit a switch that immediately polarized the windows to give them privacy. Tali pulled up a chair and sat in front of Shepard.

"So, where's this mission of yours?"

"It's a geth controlled system. From what I've heard, we're going to study a dying sun."

"That seems odd."

"I know, but I'm sure the Admiralty Board knows what they're doing."

"After that mission is through, though, you think I could see Tali'Zorah nar Rayya back on my ship again?"

Tali let out a laugh. "It's vas Neema now. And yes. I'll put in a transfer request as soon as possible. I know how important your mission is to the galaxy."

"It means a lot to hear that, Tali." The positive atmosphere that they were feeling suddenly took a change. "Thank you for what happened on Freedom's Progress."

"What do you mean?"

"When Miranda tried to control me. I-I was so close to losing control of myself. I felt disgusted. I was willing to die before harming you, but you were there pushing me to be stronger. I wouldn't have been able to free myself without you. Thank you."

"You were there for me many times before, Shepard. It is only fair that I would be there for you."

Shepard gave her a sad grin. "I was trying to tell you something before our ship was attacked."

Tali remembered that painful memory and she felt her eyes watered.

"I don't know what's happened to you in the last couple of years, but I died with regret in not telling you this. I was trying to tell you that I'm in love with you."

Tali took a sharp gasp. Tears started to come down the sides of her face. Despite how much she wanted this, she had to put his needs above her own. "Sh-Shepard..." she tried to get out. "You deserve to be happy with someone. I-I can't do that. No matter how much I- A relationship with me would be difficult at best. And you deserve someone you can kiss whenever you want. See her face whenever you want. There are billions of women out there who would make you happy." Tali was now choking on her tears in between her sentences.

"Tali, I know a relationship with you would be difficult, but that doesn't matter because you make me happy. You have no idea how much I cherished the time we spent together during our mission against Saren. The courage you showed during that mission, your selflessness. Those are all traits I've come to admire of you. You mean everything to me and I want to be with you not those billions of other women. I love you, Tali."

Tali was about to counter him, but those words finally got through to her. He... cared for her. Loved her. No amount of words was going to change that. He went against a chip imbedded in his brain to save her. He was willing to die before he would harm her. "Thank you!" she cried as she lunged into his arms. "Thank you," she followed in a whisper. "I... Love you too."

Shepard wrapped his arms around her. They savored the moment, just holding each other. "It's going to be just like old times during this mission."

"Better than old times," she corrected.