Dr. Chakwas was the first one on the Normandy to know.
She would be in her office when Shepard would burst into the med bay, Kaidan pale and trailing behind her. The first time it happened, the good doctor came out to see what was going on.
Dr. Chakwas was used to helping Kaidan with his L2 implant headaches, but the Commander was apparently not. "I need some aspirin and a cold cloth, Doctor. Now!" she demanded, helping Kaidan lay on one of the beds.
Chakwas nodded and went to her cabinets. She overheard Kaidan say to Shepard, "You're going too far. 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." She handed him water and a blue pill.
He didn't respond, just obeyed her command. The doctor stood awkward, trying not to let her bewilderment show. All this for a headache?
Shepard sat down in 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 and she went inside. 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 was headed back to the med bay with supplies when she spied them through the window. Kaidan's head rested in Shepard's lap as she stroked his hair, a cold press over his eyes.
It clicked for her. She had made that pass at Shepard, but had always felt that the reason she said no was because of someone else. Kaidan. Of course. She would want another human like herself.
And there had been rumors, but nothing concrete. No one could say why they felt there was something between them. Shepard was professional. There were 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 were often whispering by the lockers, that they tended to eat together, and that Shepard smiled more when he was around.
Liara decided to take her supplies below, waiting for them to leave. She didn't feel it was right to interrupt them. Even Commander Shepard deserved a moment of peace.
When Shepard's body was brought in to the Cerberus labs, Miranda took the task upon herself to remove Shepard's armor, or what was left of it. Her skin was shriveled from the lack of oxygen, and her armor was in shreds. Surprising, some of her clothing underneath was still intact. As she removed her bra to hook up wires to her chest, a piece of paper fluttered out.
Miranda picked up the paper off the operating room floor and turned it over. It was 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 was around her shoulders, his head tilted in her direction but his eyes on the camera. It was shocking, to not only find this but to also know that the great Commander Shepard was sleeping, or at least involved, with one of her crew. From what Miranda knew of the Commander, she always followed orders, except when it came to saving the universe.
She didn't know what to do with the photo. Shepard's eyes, the happiness in them, haunted her. It was difficult to see any resemblance to the body that laid on the table. Her hair had been burned off during her descent, and her teeth were shattered. She could read fear in her dried eyes in their sockets.
Miranda put the picture in her pocket. It would be best to burn it. She didn't want to tarnish her memory to the other members of Cerberus.
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 had never seen the Commander like this.
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?"
"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 and squeezed. They sat in silence as her sobs died out. He looked down and saw that she had fallen asleep.
Garrus carried her up to the cabin, taking care that no one else saw her like this. He was surprised 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 would go visit Garrus. The two of them kept quiet, and no one else on the crew knew about Shepard's 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 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 containers.
Shepard is flustered and pushes 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.