Dr. Karin Chakwas was the first one on the Normandy to know.
Shepard burst into the med bay on a monthly basis, Kaidan pale and trailing behind her. The first time, the doctor came out to see what happened.
Kaidan solved his L2 implant headaches with solidarity, which made the Commander's presence that more confusing. Dr. Chakwas knew what Kaidan preferred for relief, but that didn't stop the Commander from barking orders. “I need some aspirin and a cold cloth, Doctor. Now!” she demanded, helping Kaidan onto one of the beds.
Chakwas nodded, a little bewildered, and went to her cabinets. She overheard Kaidan say to Shepard, “You’re going too far, Shepard. It’s just a headache.”
She walked back over and handed the items to the Commander. Shepard slapped the cloth across his forehead. “I need everyone in prime condition. Now, take this.” Shepard handed him water and a blue pill.
He didn’t respond, just obeyed her order. The doctor stood by, trying not to show her confusion on her face. All this for a headache?
Shepard sank into the chair next to Kaidan’s bed. The doctor turned back to her office, but not before catching a glimpse of Shepard’s hand brushing at Kaidan’s cheek.
She smirked as the doors opened. She wouldn’t say anything. An independent woman like their Commander, she needed someone to worry about every now and again.
Liara was next. She headed back to the med bay with supplies when she spied the two through the window. Kaidan’s head rested in Shepard’s lap as she stroked his hair, a cold press over his eyes. The look of serenity on Shepard's face, she never saw anything close to that on the Commander's face before.
It clicked for Liara. She made that pass at Shepard, but felt that the reason she said no was because of someone else. Kaidan. Of course. She wanted another human like herself, and Kaidan wasn't without his charm.
And there were rumors, but nothing concrete. No one could say why they felt there something existed between the Commander and her lieutenant. Shepard remained professional, never any touches or longing glances between them on missions or on board the Normandy. Instead, all anyone could say was that she and the Lieutenant often whispered by the computer bank, that they tended to eat together, and that Shepard smiled more when he was around.
Liara decided to take her supplies below deck, wait for them to leave. She didn’t feel right interrupting them. Even Commander Shepard deserved a moment of peace.
When Shepard’s body arrived the Cerberus labs, Miranda took the task upon herself to remove Shepard’s armor, or what remained. Her skin shriveled from the lack of oxygen, and her armor shredded in the breach of atmosphere. Surprising, some of her clothing underneath the armor survived. As she removed Shepard's bra to hook up wires to her chest, a shining piece of paper fluttered out.
Miranda picked up the paper off the operating room floor and turned it over. Not paper, but a photograph. The Commander sat at a table, smiling at the camera. Beside her, Miranda recognized a member of her crew, Lieutenant Kaidan Alenko. His arm stretched around her shoulders, head tilted in her direction but eyes on the camera. Miranda shoved down her shock at the find, not only the discovery of the photo but to also know that the great Commander Shepard slept, or at least involved herself, with one of her crew. From what Miranda knew of the Commander, she stayed strict on Alliance regulations.
She didn’t know what to do with the photo. Shepard’s eyes, the happiness in them, haunted her. The body on her operating table made it difficult to see any resemblance to the young woman in the photo. Her hair burned off during her descent, and her teeth shattered. Blinding blue stared into the light fixture in the ceiling, what remained of her eyes as they sat dried in their sockets.
Miranda put the picture in her pocket. It would be best to burn it. She didn’t want to tarnish Commander Shepard's memory to the other members of Project Lazarus.
Shepard always wondered about the picture in her cabin, about how anyone knew about her and Kaidan. She never asked.
Garrus wished he didn’t know.
After their mission on Horizon, he found Shepard belligerent in the main gun. “Everything okay?”
“Garrus, you came with me. Why didn’t Kaidan?” She looked down to the near-empty bottle of vodka in her hand. He never saw the Commander in a state like this, her usual composure nonexistent.
He slunk to the floor next to her. “I don’t have an answer for you. Neither does that bottle.” He tried to grab it from her, but she held tight.
“We’re still the good guys. Right?”
Garrus rolled his eyes. “You would think.”
She leaned her head onto his shoulder. “I just…I thought he cared.”
“We all care about you, Shepard.”
“But, it’s different.” She took another swig from the bottle, draining the last of it. “With him, it’s always been different.” She started to cry. Unsure of what to do, he put an arm around her shoulders and squeezed. They sat as her sobs came and went in waves. When she went silent for more than fifteen minutes, he glance down to find that she fell asleep against him.
Garrus carried her up to the cabin, taking care that no one else saw her like this. As he passed her desk, surprise flooded his thoughts to see the picture on her desk flicker to Kaidan’s face. Suddenly, he understood.
It became a routine: find Shepard drunk and passed out, carry her to her cabin, glare at Kaidan’s face on the way out. When Tali joined up, she became part of the routine, sometimes finding Shepard first when she went to visit Garrus. The two of them kept quiet, and no one else on the crew knew about Shepard’s gradual unraveling. And together, Garrus and Tali learned to hate that picture of Kaidan.
By the time James boards the ship, their relationship is almost common knowledge among the crew. James doesn’t think there will be one, not anymore. He witnessed firsthand their fighting on Mars, Shepard punching Kaidan in the jaw and storming off to take out more Cerberus bastards. Even though Shepard stood by his side after he was injured, it seemed like they were irreparable.
Yet when Kaidan joins back up on the Normandy, James finds them making out behind some cargo crates.
Shepard flusters and shoves Kaidan away. “It’s not what it looked like. We were…”
“Practicing up-close combat,” Kaidan cuts in, cheeks scorched.
“Can I go next?” James jokes.
Shepard’s face goes red. He’s not sure if it’s from embarrassment or fury. “Get out of here, Lieutenant!”
“Sure thing, Lola.” He laughs as he saunters away. He can hear a flurry of whispers between them as he leaves. He doesn’t catch them again.