I always thought it would take a salient, immediate chance of losing Thane to make Shep realise what he meant to her, so here's my take on how it might play out.
Disclaimer: Characters, world, etc (pretty much everything but the situation) are not mine and all rights etc to Bioware
Gone
The doors to Life Support swished shut behind Aurora Shepard as she scanned the datapad in her hand. 'A small group can do it,' she muttered as she approached the table where former assassin Thane Krios usually sat in meditation. 'Get in and out fast enough, and most of the damn pirates won't even know we've been and gone.'
'So, what do you think?' The commander of the Normandy laid the schematics down on the table. The layout of the Blue Suns' Lorek base was simple, affording the team to opportunity to mount a quick smash and grab, rather than their usual thorough sweep. 'Thane...' Shepard's voice trailed off as she looked up and realised the seat usually occupied by the drell was empty.
Shepard had already asked for Garrus' thoughts on her plan for a lightning strike to extract Cerberus' lost data, so she knew Thane wasn't up in the crews' quarters. Nor was he in the CIC, she was certain. The taciturn drell didn't socialise with the other specialists in the team, let alone with the general crew of the Normandy. In fact, she'd bet a large sum of credits on the fact that she was the only person on the ship that he'd had a real conversation with – a conversation that wasn't directly focussed on the mission at hand anyways.
'Oh for crying out-loud Thane! Why'd you pick now to go walkabout?' Sighing in exasperation, Aurora grabbed the datapad off the table, glancing at the starry vista out the viewport as she straightened. In truth, she was pleased that one of the more reticent members of her crew had left his solitary quarters and was somewhere on the ship, possibly talking to the others. Trying to think of where she might find the philosophising assassin, she wondered if maybe he was on the bridge with Joker or in the lab with Mordin.
She had already turned towards the door when she finally registered the form she had seen reflected in the bottom of the viewport.
As she turned sharply towards the far corner, Aurora saw Thane's lithe form stretched out on the low cot beside the shelf where he kept his few personal belongings. Looking fondly down at the drell in his repose, she smiled and stepped closer. Several weeks had passed since she had met the assassin on Omega and she had not yet had the opportunity to look at him, really look at him, without being observed herself.
Usually the vanguard of the team, using either her pistol or engineering skills at the forefront of any action, Aurora was not nearly so confident when the shooting stopped. It took crisis and chaos for her need to provide leadership to overpower her natural reserve. In social situations, however, it was her shyness and fear of making a faux pas that ruled her actions. So it was that she had focussed on limiting herself to polite glances and casual eye contact during her conversations with Thane instead of openly ogling the first drell she had ever met.
Now though, she was presented with the perfect opportunity to indulge her curiosity without interruption, and it was not an opportunity she was going to pass up.
Shortly after Thane agreed to join Shepard in her mission to stop the Reapers, Kelly Chambers had commented on his cool confidence and the fact that she couldn't decide whether the former assassin was sexier than he was scary, or vise versa. While she didn't admit it to the yeoman or even herself at the time, there had been something about the man that drew Shepard's attention.
But now, alone with the sleeping drell, she had to admit the Kelly was right and that even in rest, Thane exuded an alien sense of danger. The reptilian cast to his features and tint of his skin added to his foreignness, but the tattoo-like black markings made her think of the tribal tattoos once seen on Earth.
Letting her gaze linger on his face, Aurora wondered at the contrast between the rough-looking, scaly skin of his brow and the smooth, silky red folds on his cheeks and throat. Her eyes followed the line of his neck and traced the freckling of brown spots across the exposed top of his chest. The tight leathers covering the rest of his body did little to hide his graceful form, body whipcord-tight with wiry muscle. Some of the proportions were slightly different, Shepard mused, but he didn't appear to be built much differently than an athletic human male. Although, with those narrow hips and muscled chest, she found she was reminded more of a lithe greyhound ready to race off in pursuit of its prey.
Over the weeks after Thane's recruitment, Shepard sought to learn more about the enigmatic man who preferred to spend his remaining time alone in Life Support, rather than with the others. At first she had avoided the awkward topic of his condition, but when Thane himself had broached the topic she was surprised by his calm resolve. Thane had assured her that he still had months left in which to help her in her mission and atone for his past. It had been hard for her to reconcile the thought that he was dying with the apparently healthy, composed man who had offered her his services mere moments after he had descended like a vengeful wraith from the ceiling, expertly killing Nassana Dantius and her guards.
Even harder to reconcile was the fact that she would lose the comfortable friendship that had grown between them to something as indiscriminate as Kepral's Syndrome, something she could do nothing about. Neither her skill with her weapon nor her technical expertise could protect Thane from the ravages of the condition, and her impotence only made the prospect of losing him harder to accept.
The sense of loss she felt when she thought of the fate that awaited her new companion had nearly been enough to make her retreat from the friendship he offered. But instead of staying away and insulating herself from the pain, she found she was drawn back again and again to Life Support and their introspective conversations. And so she promised herself that she wouldn't let Thane see her distress and that she would make the most of the time he had left, helping him to make peace with himself.
She was still enjoying the chance to admire Thane without him being aware of her scrutiny when she registered that he was incredibly and unnaturally still; so still that she was unable to tell if his chest had moved while she had been watching. She had never before seen Thane sleeping and stretched out, fully dressed with his long graceful hands folded just above his stomach, he resembled nothing more than a body laid out for burial. Dread constricted her chest, making it feel as though she had just been kicked in the sternum.
'Thane... no.' She whispered his name, barely able to hear herself over the sudden rushing of blood in her ears and the pounding of her heart. 'Check,' she told herself, barely able to breathe through the burgeoning fear. 'It could be a mistake, must be a mistake. Check. I need to check.'Shepard's legs gave way, involuntarily folding under her as she stepped closer to the cot in the corner. She knelt awkwardly by Thane's side, looking intently for any sign of life – a flicker of an eye, a whisper of breath, anything. But there was no movement to be seen. Thane's body was as still as though carved of stone.
'Please, no... Not yet. Please, not yet.' Slowly, afraid of what she would feel, she stretched out her hand and placed it lightly on the bared top of the drell's chest. The leathery ridges of his skin were cool and firm under her fingers. Regret threatened to swamp her as she knelt beside the cot, her hand still on Thane's cool chest. Her other hand moved to cup his cheek, thumb slowly stroking the darker scales under his eye.
It was too soon. Too soon for him to be gone already.
She was nearly overwhelmed by the emotions that welled up as she thought of how Thane's steady presence had quickly become her lifeline, anchoring her when she was at risk of losing herself. How much she needed their philosophical debates to stimulate and challenge her. How she had come to rely on him and Garrus always watching her back, protecting her from her own impetuousness as much as from their enemies.
She hadn't said anything to Thane, hadn't told him what he meant to her, believing that the end was months away and that they still had time to explore the connection between them – but now he was gone and it was too late to tell him just how she felt.
As she struggled to hold back bitter tears, Aurora became aware of a faint, intermittent throb beneath the hand on Thane's chest.
Deep in a meditative trance, Thane Krios was thoroughly unaware of the distress his stasis was causing.
As he slowly drifted up from his introspection, Thane felt an unusual warmth and weight on both his chest and cheek. The pleasant sensation made him smile reflexively as he opened his eyes. Momentarily blinded by the lights, it took time for him to register the form beside him.
As he blinked owlishly at his commander, he felt her fingers run lightly across his brow and then withdraw. The touch was nearly imperceptible and if not for the faint trail of warmth it left on his skin, he would have thought he'd imagined the caress. Not wanting to lose the remaining contact, he placed his hand atop the one she still had on his chest.
'What have I done to warrant such an awakening?' Aurora felt Thane's heartbeat strengthen and chest resonate with his question as he surfaced from his state of near-hibernation. The words were spoken lightly but the pressure of his hand on hers belied his levity. His face was serious as his eyes met hers.
'Thane,' Aurora paused as she struggled to speak past the lump in her throat. 'You were so still. I thought you were gone and...'
'And you thought you'd check on me? I appreciate your concern but there is no need – I was simply meditating.' The intensity of Thane's gaze didn't waver as he searched her eyes, bright with unshed tears.
'I'm sorry. I didn't mean to disturb you.' Shepard's cheeks flushed crimson and she turned her face away in embarrassment. 'I'll just, um, leave you to your thoughts then,' she mumbled as she tried to pull her hand free and flee.
His hand tightened on hers, holding her in place as he raised his free hand to cup her cheek. Gently turning her head towards his own, he spoke softly. 'Shepard, it's been a long time since anyone has cared enough to check up on me. I don't know what I've done to deserve your friendship, Siha, but for what it's worth – thank you.' Aware of her discomfort, he gave her hand one last quick squeeze before releasing it and gracefully rising from the cot.
Turning away to seat himself at the table, Thane allowed Aurora a moment to compose herself. A quiet sigh escaped his lips as he thought of how at least he now had this memory to keep him company on his long, lonely nights. The memory of the concern written so clearly on her face and the warmth of her hands on his chest and brow.
Forcing his thoughts from the softness of her cheek under his hand, he changed the subject and asked, 'Now, Shepard, you came down here to talk to me about something... .'