Author's Note: Legionary Prime and Agent Rhode Island gave me ideas for this chapter, and for that I thank you. Sorry for the delay but writers block kept me from posting this Sunday or Monday. Also, everything in italics are memories.

Chapter Thirty Eight: Goodbye

Hackett had come aboard the Normandy about an hour ago. Everyone saluted and showed the proper respect, but he could hear the whispers. Shepard's crew was one of the most elite groups of people ever assembled, but they were still uneasy at his presence. Hackett knew that they understood that he didn't show up on ships to just say hello, even to the great Commander Shepard. They understood that something was happening, but what hung in the air was if it was good or bad.

Hackett liked Commander Shepard. In fact they would probably be good friends if work wasn't in the way. That wasn't the point though; some of the worst criminals are very likeable. Not that Shepard was a horrible criminal, but the law wasn't something that only a few people had to follow. Killing three hundred thousand people would have dire consequences. He just hated doing this to someone who was such a good influence over everything he touched.

"Shepard, I don't know how to say this...but you're going to be a wanted criminal in seventy two hours," Shepard was shirtless with bandages circling his entire torso. He sat on one of the Normandy's med-bay beds.

"What?!" Shepard looked up at Hackett.

"The Alliance is processing your arrest warrant, and in seventy two hours, if you haven't turned yourself in, then..." Hackett stopped there.

"Sir, I had to kill those Batarians. The Reapers would've invaded," Shepard stood up and started pacing.

"I know, and if I were in charge, I would give you a medal," Hackett responded.

"Where do I need to turn myself in?" Shepard was still pacing and now wringing his hands.

"Arcturus Station and you don't have to wear your dress uniform, but maybe it would remind people that you're not the enemy. Then from there you're going to be transported to Vancouver. That's where the Alliance's major legal proceedings happen. Listen Shepard, I don't think they can pin you on these charges. You're still a Spectre and technically you can get away with something like this. I think they know that, so they're going to make you await trial for a long time. The Batarians are up in arms about this, and the only way to avoid a war with them is to arrest you. So they'll keep you waiting until this blows over. I never told you any of this, alright?" Hackett shifted in his cold, uncomfortable seat.

"Thank you, sir. I'll remember that, and I'll wear my uniform. I appreciate you telling me in person," Shepard stopped pacing and looked Hackett straight in the eye.

"Shepard, you also need to drop your crew off. Anyone you bring with you would be considered arrested for helping a terrorist," Hackett knew this would be a low blow, but it had to be said.

"A terrorist?" Shepard rubbed his neck.

"Yes, you're being charged for genocide and being a member of a known terrorist organization," Hackett felt so bad for Shepard. Here was a man who gave everything to the Alliance, and now they were going against him.

"I see. Thank you for telling me that, sir. At least I know what the situation is, but may I ask a question?" Shepard was sitting on the table again.

"Sure," Hackett hated how he always had to talk to everyone with so many formalities. As an admiral, conversations with just friends were rare.

"Why did you tell me in person? Why not send me an email, or have someone else tell me?" Shepard wasn't looking at him in the face anymore.

"You're a good person, Shepard. You're the best soldier I've ever seen, and I like to think that we're friends. Plus you've done so much for the Alliance, the least I could do is tell you what the situation is in person," Hackett stood up, and patted Shepard on his unwounded shoulder.

"Thank you, sir. That means a lot coming from you," Shepard smiled for the first time since Hackett had come into the Normandy's med-bay.

"I'm just sorry this happened to you Shepard," Hackett sighed, "I must go now, so I bid you farewell."

"Goodbye, sir," Shepard's face disappeared behind the doors, and Hackett felt guilt settling in him. Like it or not he was the reason why Shepard had gone on that awful mission.

"Alright Chakwas, Hackett is gone," Shepard said as he entered Doctor Chakwas' back room, where she had gone to give more privacy to the officers.

"Shepard, I'm afraid I have bad news," Chakwas turned from a console towards him. Shepard sighed; today was not a good day.

"Me too, but you go first," Shepard leaned against a wall for support.

"My scans of your body are showing that you're not healing as you should. Your cybernetics weren't completely integrated into you when you received those gunshots, and that upset their rhythm as well as your natural tissue. In short your body needs time to heal, and get used to itself again. I'm sorry Commander, but I'm going to have to recommend that you go on medical leave for six months. If you don't give yourself time to heal, then your body will reject your cybernetics," Chakwas patted Shepard's shoulder.

"Well okay, makes sense to me. I need to call the crew together, I also have bad news," Shepard turned to leave into the main med-bay.

"Wait. Why aren't you yelling at me and saying that there's no way that you're going to take medical leave?" Chakwas looked over Shepard suspiciously.

"I'm calling the crew together to tell everyone, you included. Then you'll find out, but... it's not good news," Shepard's eyes held some unspeakable, heart-wrenching emotion.

A moment later EDI's voice came over the ship wide intercom," All crew report to the Mess Hall. I repeat, all crew. I will run the Normandy for the meetings duration."

...

"Is everyone here?" Shepard asked. He had his back turned to everyone.

"Yes," was said at the same time by almost everyone.

"I have some really bad news everyone," Shepard turned but kept his eyes downcast. "The Alliance is charging me with genocide and working with a known terrorist. In seventy two or so hours I will be an enemy of the Alliance," Shepard stopped to collect himself. He looked up briefly and saw the shocked faces of his crew. Some had their hands over their mouths, and other people let their jaw hang down.

"I am being stripped of command of the Normandy, and will await trial in a city on Earth called Vancouver. I am going to turn myself in, and anyone staying with me will be considered an accessory to a," Shepard swallowed hard, "dangerous criminal. So you all need to input where you would like to go and I'll try my best to get you there. Since we only have seventy two hours, we can't stop at a lot of places, but hopefully you'll be dropped off pretty close to your destination. If anyone needs creds to get somewhere, come talk to me," Shepard handed a data pad to the nearest crew member. "You can put your wanted location into this. Crew dismissed," Shepard tried to find Doctor Chakwas. When he spotted her, he waved her over.

"Oh Colt, I'm so sorry," Chakwas pulled him into a hug. "I'm still going to put you in for medical leave, though. The doctors still need to know that you require medical attention. I just can't believe that the Alliance would do this to you," Chakwas finally pulled out of the hug.

"I deserve it. I did kill three hundred thousand people, and no one is above the law," Shepard rubbed the top of his head.

"Shepard, it had to be done, this is war," Chakwas looked intently into his eyes.

"That's why I did it, but... still," Shepard was handed back the data pad with locations on it. It looked like their two drop off locations would be Illium and the Citadel.

"Alright Joker, let's go to the Citadel first," Shepard then proceeded to head for his commander cave, leaving his crew in the mess.

...

"Battle Master, I have never met someone so worthy of the enemies we have fought," Grunt carried almost nothing with him. The first stop was Illium in the sad quest of disbanding Shepard's crew. Everyone leaving for Illium was lined up, waiting to say goodbye to Shepard. He stood near the airlock so the process went faster.

"Shepard is the best Battle Master a Krogan could ask for. I don't want to join some... some washed up Battle Master's clan," Grunt's words had warmed the cockles of Shepard's heart, and then he had pissed off the Krogans that were trying to kill them.

"Grunt, the same could be said of you," Grunt only grunted and hit Shepard hard on the back. His back cracked five times and he coughed loudly. Grunt did that deep chuckle and became the first member to leave the Normandy. Legion came after Grunt.

"Shepard-Commander, we wish to wish you luck in your trial," Legion had nothing with him.

"No data available, that's what he said to me," Shepard was explaining the situation to Liara via vid comm.

"That means that he has a little crush on you," she said, winking at him. "Looks like I have some competition."

"Thank you, Legion. Where are you going from Illium?" Shepard asked the Geth.

"I hope to get back with some other Geth. Goodbye Shepard-Commander," then Legion left the Normandy.

Next up was Mordin, "Suicide squad, not so suicidal. Thank you Shepard, for getting us through."

"How was Rosebud?" Shepard had burst into Mordin's lab, excited to see his varren.

"Acting like she wasn't fed, so I fed her," Mordin stroked her head, while the spoiled varren lazily lounged in her bed by Mordin.

"That little devil, I already fed her today," Shepard shook his head at the little thing's contentedness.

"Good actor, fooled everyone," Mordin reached down again and petted her head.

"I'm going to give Rosebud to Liara to take care of. Still haven't changed your mind about caring for her?" Shepard asked.

"No, can't take her. Sorry. Liara excellent choice. Here are her bags," Mordin was carrying four bags and three were handed over to Shepard. "High maintaince thing," Mordin smiled, "Bye Shepard, we'll talk again." Then Mordin joined the increasing larger group leaving the Normandy for Illium.

Samara walked up to Shepard after Mordin. "Samara, good luck on Illium," she carried the smallest bag yet.

"I've only seen a few people with as much raw biotic power as you, Shepard," Samara was doing a circle around him.

Shepard had to stop himself from saying ma'am ,"Thanks Samara."

"Having potential doesn't mean that you're good. Do the charge again," Samara stopped behind him, and was probably disappointed in everything.

"Thank you, Commander. It has been a true honor working with you. Keep working on those biotics," with that Samara left the Normandy.

The last person to be dropped off was Zaeed,"So the big goddamn hero goes to jail. Sounds like something out of a soap opera," Zaeed carried several bags. A suspiciously long one probably held Jessie.

"Are you going to listen to my story or are you going to continue to play with the trash compactor?" Zaeed's agitated voice stopped Shepard right before he was about to launch more trash into space.

"Sorry, Zaeed. Go ahead," Shepard reluctantly left his new favorite toy to join Zaeed.

"Good, so anyways, it was just me and Jessie…" Shepard kept eyeing the trash compactor throughout his story.

"Ya , weird. My life has been like a space opera, so far," Shepard replied, before slapping off a salute ,and nodding at Zaeed as he went off the Normandy. He was the last one off at Illium.

"Goodbye Kelly, it was an honor," Shepard shook her hand, before being pulled into an enthusiastic hug. They were at the Citadel, and a little more than half the crew was getting off here. Like Illium's drop off, everyone was lined up.

"Shepard, I see that you raise fish. Would you like me to feed them when you're away?" Kelly Chambers asked Shepard, who was standing at the Galaxy Map. He was trying decide where to go.

"Thanks Kelly, that would be great. Be careful though, if you don't feed them twice a day, everyday, they will all die," Shepard shivered at the memory of his fish floating on the surface of the tank.

"Bye Shepard," Kelly nodded and headed down the ramp towards the Citadel with a bag slung over her shoulder.

"Thane, I hope the Citadel is what you need. Is Kolyat here?" Shepard shook his hand.

"You're the only friend I've had in ten years," Thane sat at his table in Life Support, looking thoughtfully over Shepard.

"Thane...You're a good friend too. I hope everything is going well with Kolyat," Shepard rubbed the top of his head nervously.

"Yes, he's here. I hope to spend more time with him, and I hope you get out of jail soon, my friend. Goodbye," Thane nodded and followed Kelly out of the Normandy.

Jack came after Thane, "Why did I always know that you were going to get arrested?" The gleam in her eyes was full of fight.

"It's so weird. Finding out I have a friend," Jack wouldn't look at Shepard. Not even a glance. "Finding out that there's someone who doesn't just want to use me," Her eyes were firmly glued to her hands.

"And don't forget it. I'm here for all my friends. You need something, you find me," Shepard then left Jack's secluded area.

"Probably because you realized that they only throw handsome people in jail," Shepard grinned down at Jack.

"A cocky asshole, as always," Jack said back. "Take care of yourself, Shepard," Jack walked out of the Normandy, she glanced back several times.

"Miranda, you were a great XO. Thank you for doing all my paperwork, also the Illusive Man thanks you," she was carrying a TON of bags.

"So do you like your steak?" Miranda asked, while they were sitting in a very nice restaurant having dinner.

"Oh it's delicious. How about your food?" Shepard took a bite of his steak. When he looked up he found her staring at him very oddly. "Is there a problem?" Shepard desperately wiped his face.

"No, just thinking," she said with a smile, and returned to her food.

"Goodbye Shepard. You have to be the best commanding officer I've ever worked with," then Miranda pecked him on the cheek and followed a quickly disappearing Jack.

"Keelah' Shepard. I'm going to miss you so much," Tali's voice sounded like she was crying. Out of everyone so far, she had the most reasonable looking bag.

"Shepard, you and Liara are sooo cute together," Tali and Shepard were eating in the Mess together.

"Thanks, Tali. But you know who you'd be really great with?" Shepard had eaten with Tali often since she had come aboard. They just happened to eat at the same time, and so they started to eat together. Their strong friendship had only benefited.

"Who?" She asked, putting down her food excitedly.

"Garrus. You two would be awesome together. You could go on dates and eat the same food," Shepard would tell Garrus something similar. His two closest friends deserved someone special.

"I'll miss you too, Tali. Life won't be the same without meals with you," Shepard patted her shoulder.

"Don't remind me about missing that. Bye Shepard," she was definitely crying now. Before he could say anything else; however, she was out of the airlock.

"So Shepard, this is where we part, huh?" Garrus was the last one to get off at the Citadel.

"Ya, guess so. I got you something," Shepard handed him a wrapped present. Garrus then proceeded to rip open the box and reveal a picture frame. One side had a good picture of Garrus looking dramatic, and the other side had a chicken that had an uncanny resemblance to Garrus, striking a similar pose.

"You're going to jail, and you might never get to see your best friend again, and as a parting present you give him a comparison picture?" Garrus stared at the picture for a few more seconds. "It's awesome, where did you get this amazing picture of me?" He then carefully placed it into his bag.

"I have my ways... so I guess goodbye," Shepard pulled Garrus into a one handed hug that lasted a fraction of a second. Garrus then picked up his stuff, nodded at Shepard, and left.

...

"Hey, Colt. Are you okay?" Liara turned to find Shepard walking up the stairs to her.

"The same since we talked after last mission," he was now standing in front of her. She took his hands and started playing with them.

"You look upset," she wouldn't be that easily avoided.

Shepard sighed and looked away, a scary sign, "I'm being arrested Liara. I'm sorry I didn't tell you over that last vid call, it was too... hard."

"Who's arresting you?" Liara stopped her hands.

"The Alliance, for genocide, and working with a known terrorist organization," Shepard took back one of his hands and ran it over the top of his head.

"Colt..." Liara was too shocked to say anything else. This development was horrible.

"After this, I leave for Arcturus Station," he sighed again.

"Shepard, we can fight this. Let's start," Liara pulled her hands away and started turning towards her console. Before she could get there, Shepard had caught her arm.

"I don't wanna fight this. I deserve it, I am guilty of both charges," when Liara turned back to face him, he wouldn't look at her.

"It had to be done. The Reapers-" Liara was cut off.

"That's what everyone keeps telling me. Ask those Batarians if they think I had to kill them, or anybody else I've affected with stupid decisions," Shepard was on a roll of self doubt.

"You. Had. To. That's all there is to it. Nothing else to consider. The Reapers arriving would've killed billions, not three hundred thousand," Liara could see that it wasn't getting through to him; he was going to go let himself get arrested. She pulled him into a desperate hug, hoping it would convey the emotions that words didn't have. They stayed like that for a long time until Shepard pulled away.

"Can you take my pets?" Shepard looked up for the first time.

"Of course," Liara smiled when she saw how much Shepard had perked up.

One hour later everything had been brought in for Shepard's pet. Rosebud had an unbelievable amount of bags. The hamster, Boo, had more stuff than she did. The fish also had boxes with supplies. After Shepard had brought everything needed for his animals, he handed Liara three large pieces of paper with instructions on them.

"So, remember the fish need to be talked to every time you feed them. I read on the extranet that it helps them digest food. If you're gonna buy Rosebud something, make sure it's pink. That's the color that goes best with her pelt color," Shepard would've continued but Liara silenced him with a kiss.

"Don't worry, I'll take good care of them all," she whispered after they had broken from the kiss, needing oxygen.

"Alright, I'll get Rosebud," Shepard left her ship. The hamster and the fish had already been brought in. A moment later, a varren next to Shepard came through the door. Rosebud had on a pink jacket, with a pink collar, and a pink leash. "Sometimes she gets cold. So if she starts to shiver, put her coat on," Shepard had opened one of the bags and took out a bed that he laid next to Liara.

Colt kneeled next to Rosebud and looked her straight in the eye. "You be good now, Mama's gonna take care of you while I'm gone. Be good for her, she has a lot on her plate without you causing trouble," when Shepard finished, Rosebud licked his whole face. He stood up and led her over to Liara.

"Hi Rosebud, I'm gonna take care of you while Sheps away, okay?" Rosebud's response was to lick Liara's hand and then lay in her bed. Shepard looked at her for a little and then turned his attention back to Liara.

"I'm gonna miss both of you, so much," Shepard wrapped Liara in a huge hug. Liara breathed in his intoxicating scent. Shepard buried his face into her neck. "Visit me, okay? Although I would understand if you didn't. It's not exactly dignified telling someone you're going to visit your boyfriend in jail...I guess I should go now," he said after a much too short time period. Then like that, Commander Colt Shepard went off to jail.

...

"Shepard, you're looking good," Joker whistled at Shepard when he heard footsteps behind him, and took in his whole appearance. Shepard wore his full military uniform. He wore the traditional officer's hat with a gold Alliance symbol on it. The Star of Terra hung around his neck, the ribbon it was attached to was concealed by his collar. Other medals and bars of color were attached on his right side. The N7 logo was also sewn on the right side. His shoulders had a stiff padding on the outside that all Alliance uniforms had with gold thread as the border. Black material was tight against his sides, with gold highlighting the borders. A gold chain connected his right and left side, and the jacket's opening was more left than centered. On his right hip he carried a saber. The scabbard was simply blue with a gold ending.

"Enjoy it Joker. This is probably the only time you'll ever see me in full uniform. I've never worn The Star of Terra or my saber before. That's how rare this is," Shepard replied, adjusting his saber slightly.

"I am enjoying it, but probably not as much as Liara would. Let me take a picture and send it to her," Joker started to mess with his omni-tool. "Ready?" He asked aiming his omni-tool at Shepard.

"Yep," Shepard's back was straight as a board and he saluted the camera. "Good?"

"Oh yes. Didn't want to miss the opportunity," Joker turned back around in his seat.

"We have arrived at Arcturus Station. Alliance police are requesting permission to come aboard," EDI's voice echoed through the empty ship. The only people left were EDI, Doctor Chakwas, Ken, Gabby, and Joker.

"Permission granted," Shepard waited near the airlock for them. Minutes later the door slid open to reveal Alliance MPs.

"Commander Shepard?" One of them asked.

"Yes, sir," Shepard replied straightening out his uniform.

"You're under arrest. Please turn around," a different MP walked up with handcuffs. Shepard turned around and felt the handcuffs tighten. They led him off the Normandy and immediately Shepard was met with the blinding flashes from cameras.