2 Months Later
Shepard stands at the edge of a cliff, a small fire burning in front to her. Katherine stands behind her as Shepard holds a picture of herself and Garrus. Without a word, Shepard crouches down and tosses the picture into the fire, watching it burn to ashes. She then takes out her Alliance dog tags, the ones Liara gave her, twice now, and digs a shallow hole next to the fire. Carefully, she places the tags inside and covers them with desert sand, to bury them. This action is a silent tribute to the end of a chapter in Shepard's life.
She turned to her new friend, Katherine Hudson, whom she had begun referring to as "Kathie." Of all the people currently in her life, Kathie is the only one who refers to her as Shepard in private.
Kathie was leaning against a tree, reading a report from Phoenix. After Shepard's recent episode, she had gone to Kathie's apartment and poured her heart out, even admitting to her attempted suicide. Kathie had held her as she broke down, and Shepard even admitted she had never cried so much in her life before now. Now, as she looked at her only remaining friend, Shepard felt grateful for Kathie's presence in her life.
Without a word, Shepard walked over to the tree and sat down next to Kathie who was sitting down now, the two of them sitting in comfortable silence as they watched the sun begin to set over the horizon.
Shepard gazed out beyond the cliff; her mind preoccupied with recent events. After her emotional breakdown and heart-to-heart with Kathie, Shepard had made the decision to join Phoenix. However, she had one condition: she would only agree to joining Phoenix. Only if she got to see the Alliance burn. Kathie had sent a message to her contacts, and after a week, the response had come back: "Welcome to Phoenix."
Shepard knew that the Alliance had a stranglehold on the galaxy, despite suffering massive losses in the war against the Reapers. With the help of the Reaper husks and the memory of the martyr Commander Shepard, they hold most of the political power. The Turian Hierarchy is little more than a vassal to the Alliance, and only a select few nations were allowed access to Reaper technology. The rest were either blacklisted for being too close to Shepard or deemed untrustworthy.
As Shepard thought about the state of the galaxy, she couldn't help but feel a sense of anger and frustration. She knew that joining Phoenix was the right decision, and she was ready to do whatever it takes to bring down the Alliance and bring about real change.
As the sun set, Shepard leaned against a tree, enjoying the tranquility of the moment. She had managed to secure an extension of her curfew until morning, so she decided to spend the night outdoors with her friend Kathie. It had been a while since Shepard had slept under the stars, and she relished the opportunity to do so again.
Kathie, however, remained absorbed in her padd, seemingly oblivious to Shepard's attempts to get her attention. Shepard called out to her friend multiple times, but to no avail. Finally, she decided to take matters into her own hands and gently retrieved the padd from Kathie's grasp, stowing it away in one of their backpacks.
Kathie finally turned towards Shepard; her expression surprised but not to upset. Shepard offered a sheepish grin, hoping her friend wouldn't be too annoyed with her. They settled back against the tree, enjoying the peaceful night and each other's company.
Next Morning
Shepard and Kathie ride their bikes back to their apartment complex after a very pleasant evening. As they dismount and prepare to part ways, Kathie tells Shepard she'll catch up with her later. Shepard watches as Kathie enters her apartment before turning her attention to her own apartment as she entered she saw one of her guards at her bar. The guard reassures Shepard that she's not in trouble, just a few minutes late but nothing major, and hands her a letter before departing. Shepard opens the letter, surprised to see it's from someone she hasn't spoken to in years, but still considers a close friend.
"Shepard, I hope this letter finds you well, or as well as you can be given the circumstances. I'm truly sorry for what's happening to you. Just know that those of us who know about your situation are doing everything possible to help you or at least make it bearable. As for me, I resigned from the Alliance a few weeks ago by simply leaving. My dad is furious with me for doing so, but there's little he can do these days. I wish I could see you, but it's not safe for either of us. I managed to get one of your guards to deliver this letter to you. If you need me for anything, you can reach me on our old comm channel and leave a short message. Your old friend, Sara."
Shepard read and re-read the letter, hardly believing what she was seeing. She had thought she had lost everyone, but now she had two friends looking out for her. She couldn't help but laugh at the thought of Hackett being mad at his sneaky daughter, Sara.
Shepard heads to her bedroom and begins to pack a small duffel bag. Tonight, Phoenix is coming for her and Kathie. Shepard carefully hides the bag, just in case the Alliance guards decide to conduct an unscheduled search.
Around 10:30 P.M.
Shepard and Kathie are waiting for the green light from Phoenix. Kathie arrived two hours ago with a duffel bag, taking out two Avengers rifles and handing one to Shepard just in case. They talk while they wait, Kathie is asking Shepard if she's ready. Shepard admits that she's not; it's been almost two years since she's been in combat. Suddenly, the light on Kathie's watch turns green, and Shepard and Kathie grab their rifles and head for the front door. As they left an as expected, the Alliance was ready for them, with four shuttles waiting and Alliance Soldiers aiming their rifles at them. An Alliance officer orders them to drop their rifles and surrender, but Shepard fires at the Alliance instead. The soldiers take cover behind civilian vehicles and return fire, but Shepard continues to expose herself from cover behind some civilian vehicles, is shooting back at the Alliance soldiers.
Suddenly, pure pain shot through Shepard's body as her prosthetic arm malfunctioned. She glanced down at the arm and instantly knew that the Alliance was responsible for it. Despite the excruciating pain, Shepard made her way over to Kathie, who was firing fiercely at the Alliance. With a determined look, Shepard drew her pistol and fired.
After several minutes of intense firefighting, Shepard and Kathie spotted two approaching shuttles. The shuttles' unfamiliar colors made Shepard assume they belonged to Phoenix. As the shuttles landed, the Alliance turned their attention to the six Phoenix operators disembarking from them. Kathie assisted Shepard as the pain from her malfunctioning arm became unbearable. In an act of desperation, Kathie removed Shepard's prosthetic arm to relieve her some of the pain.
As they headed towards the shuttle, Shepard returned the favor by using her pistol to take out any remaining Alliance officers who tried to target the shuttles. Despite the odds stacked against them, Shepard and Kathie made it to the waiting shuttles.
As Shepard boarded one of the shuttles, Kathie followed closely behind. Suddenly, an Alliance soldier fired a rifle and round struck Kathie in the shin, causing her to collapse to the ground. The medic rushed over to attend to her while the other shuttle stayed back to eliminate the remaining Alliance soldiers.
Shepard knelt by Kathie's side as the medic bandaged her wound. As they helped Kathie onto the shuttle, Shepard's mind raced with disbelief at what she had just done. Though she may not have killed any of the Alliance soldiers, she had fired her weapon with the intent to do so.
Shepard couldn't shake the overwhelming feeling consuming her, even as the vehicle took off. As someone committed to fighting for what was right, she couldn't help but question the morality of her recent actions. Although she had shot at Alliance soldiers, she felt no remorse. Phoenix was taking her to an unknown destination, but she couldn't even muster up the energy to care. It was then that Kathie noticed Shepard's troubled expression and reached out to place a comforting hand on her forearm.
"Hey you, okay?" Kathie asked, her voice laced with concern and some pain due to being shot.
Shepard forced a weak smile. "I'm fine," she replied, but even she could hear the lack of conviction in her own voice.
"You don't seem fine," Kathie said gently, her hand still resting on Shepard's arm.
Shepard sighed, feeling the weight of her internal struggle. "It's just...I don't know. I've always been willing to do what it takes to get the job done, but shooting at our own people? It doesn't feel right."
Kathie nodded, understanding. "I know it's hard, but sometimes we have to make difficult choices in order to protect what's important. You know this. You done similar things before. You did what you had to do."
Shepard nodded, grateful for the reassurance. "Thanks, Kathie. I just hope I made the right choice."
Few Moments Later Aboard a Phoenix Warship
Shepard was startled as a Quarian in a light jacket walked into the medical bay without her environmental suit, only wearing a sleek black respirator. Shepard couldn't help but wonder how the Quarian was managing to be outside her suit but decided to focus on the situation at hand.
The Quarian introduced herself as Phoenix Director Robyn Harper, leaving Shepard even more shocked.
"Director Harper, it's a pleasure to meet you. Thank you for getting me out of there," Shepard said gratefully.
"Of course, Commander. What the Alliance did to you goes against everything that countless young men and women gave their lives to protect. Phoenix aims to create a better future, and with your help, we can accomplish that," Director Harper said, while Kathie sat up on the medical bed.
Shepard couldn't ignore the nagging feeling that the Phoenix ship was somehow connected to Cerberus. She decided to confront Director Harper and asked her directly, "Be honest with me. Are you Cerberus? This ship screams Cerberus."
Director Harper took a deep breath before responding, "No, we're not Cerberus. We used to be part of Cerberus, but we left when the Illusive Man betrayed Earth and humanity. We formed Phoenix. I led the Science Division when we were Cerberus. I even oversaw Miranda's Lazarus Project, and even recommended her, to the Illusive Man to lead it." Shepard was taken aback by this revelation.
"You've saved me twice then... thank you, Director," Shepard said gratefully.
"Actually, Miranda brought you back the first time. I just signed off on the paperwork. But I owed you, Shepard," Director Harper said. Shepard was puzzled by this.
"Don't you remember?" Director Harper asked, noticing Shepard's confusion. Shepard shook her head.
"The Alliance and flotilla were part of a project that your father led alongside my parents. It was designed to boost our immune systems..." Shepard looked as though she had seen a ghost.
Shepard stared at the figure before her in disbelief. "You're her. I thought you were killed?" Shepard asked in shock.
"The same can be said about you. Twice now. Turian Blackwatch killed them. Cerberus saved me. Raised me to love earth. I am still doing that Shepard. We have much to talk about. For now, rest. And tomorrow we will plan for the coming fight and get you fitted with a new arm." With that, she left the med bay, leaving Shepard to ponder the situation.
Turning their attention to Kathie, who was lying on a medical bed now with a white bandage wrapped around her injured leg, Shepard walked over to her. Kathie met Shepard's gaze as she stood over her, and without a word, Shepard leaned down and kissed her on the lips. Kathie eagerly returned the kiss, and after a few moments, they broke apart with beaming smiles. As Shepard walked away to rest for the coming few days or even weeks.