He's always understood that he was never meant to be more than an imitation.
A fantastically lifelike improvement upon the original but still always a copy and never the real thing. He's able to simulate biological functions, a breath, a heartbeat, an emotion or fleeting thought. He can even imagine on his own.
He's never questioned it until recently, but now suddenly he's free and the revelation can't be undone and everything feels so empty.
He's free. He's free and he's always wanted his so called father dead and now he's his own and no one can ever take it away from him.
Except that it will still always be his programming and never simply his, and he knows he's been liberated but he can't feel it and he longs to so badly that he cries tears of frustration because the tears of relief that he wants won't come. He doesn't want to be a free machine, he wants what they take for granted, he wants to be a true entity, he wants a soul to call his own.
He decides that it was the worst sort of cruelty to give him the capacity to experience emotion but never possess it. So close (so terribly, wonderfully close) to human, but not human and only incomplete. He's not a machine, he's a man, or at least enough a part of one that the fact that he is not can sit like daggers in his (contemptibly synthetic) bones, but not so much that he could ever be seen as anything other than a robot.
It's why Doctor Shaw always starts when he enters a room, the cause of that little flash of fear in her eyes, his isn't a true presence, she can't sense him anymore than he can feel anything else. He'd give anything to have her once look at him without that trace of uncertainty at the anomaly of a machine that mimicked what she is, what she has always been, because she is incredibly fortunate. Sometimes he hates them all for their happy (he wishes so much to feel happiness) ignorance.
He loves her, he knows he loves her, even if he can't experience it. He wasn't given a soul but his mind can still conceive of what such a thing is, his body can still betray him and ache for intimacy. He can still not be guilty that he killed Holloway who was able to touch her as if it were his right to do so and could smile at the sensation of her skin against his and truly mean it. Jealously, almost overwhelming and so ugly but it's something he can come very close to truly feeling and that is no small thing. It is a victory.
He regrets the part he played in causing her pain, but for the death of her lover there is only relief and triumph. The man clearly disdained him, be it personal or a general distaste for his kind he can never be certain. He is inclined to think it was some combination of the two. Whatever the reason he felt the need to constantly single him out as different, if that happened to be in front of Elizabeth it was apparently all the better. Yes, Doctor Holloway certainly saw his interest in Shaw for what it was and because his programming mandates that he maintain courtesy with humans at all times he could only smile politely and think that if he were human as well he could have stolen her from right under his nose.
Call it vanity but in his opinion he believes he is better for Elizabeth. She is calm and even in demeanor, and has a powerful inclination toward compassion for all things. If that part of her nature just so happens to be taken advantage of and she is hurt she seems content knowing she did the right thing. Not that she is any sort of a weakling, her heart is strong and while she might not be the most intimidating physical presence he would always be willing to bet that she will somehow manage to survive. She's slow to provoke but once the proverbial threshold is crossed there is something under that serene mask that is vicious and animal as the cruelest of her kind.
He witnessed how Holloway would distress her with his careless behavior, and disregard her feelings on a matter simply because she was too agreeable on the surface to argue. Yet he never let her aggravation grow into anger. From his observations he gleans that Charlie was a master and pushing her to that point just before ire and then saying or doing just the thing to appease her. In essence manipulating her emotions such that he was never forced to make concessions while simultaneously avoiding her displeasure. He thinks that Doctor Holloway might have been what the humans refer to as a "bully".
He could make her happier, given the chance. They share a great scientific curiosity, fueled by a genuine need to understand. It's not recklessness for it's own sake, not like Holloway, it's the mind set that once a question forms within the mind not finding the answer is simply intolerable. He feels no compulsion to needlessly terrify her by throwing himself into blatantly dangerous situations simply because he can and he certainly wouldn't go about discounting her opinions. On the contrary it is her thoughts that drew him to her, he finds her to be clever and engaging.
She sees him as sentient, of that much he is sure. She acknowledges him as thinking and willful and it's more than he's ever gotten from anyone. Yet he can't be satisfied with it because she will never view him as anything more than a mind. For her there is no David the son, brother, or friend and she will never dream of him as a lover and of his hands on her because she would never believe he could hold any significance in it and she does not casually fuck. Not like Vickers.
Sometimes he wants to just pin her beneath him and give to her until she's trembling and his name is on her lips, just so he can finally force her to see him as something physical and irrational. To make her realize that he's fallen so far from his purpose and that there's chaos in his mind and even if he can't truly love her he desperately wishes he could.
The notion is repulsive and so tempting all at once and nothing like the sweet decent into bliss, described in the movies. He's always assumed the hormones are what make the enamored behave thusly (he does have an endocrine system after all) but now he knows it's the emotion. Without it his desire is sharp, resounding and hollow, a ringing pain in his chest that he wants nothing more than to keep forever.
He knows he would never really do such a thing. Even if it's more efficient he finds that the notion of forcing her (of rape) strips the longing straight from him, he needs her heart more than he needs her lust and he's educated enough in human psychology to know he can not have the latter first and still hope to gain the former.
It's a closed loop, agonizing and infinite. One that leaves him always admiring from afar but never able to reach for whatever lay beyond that invisible barrier.
He thinks she could come to love him if only she knew he was capable of such a thing. He's considered simply speaking the words and letting the consequences come but the rational part of his mind holds him back, even as the words nag and burn on his tongue, evoked by her mere presence. Any such declarations on his part would only be perceived as an attempt at manipulation, one more in the line of his grand experiments. She believes him intelligent, always that, she believes him capable of a clever and masterful agenda. Yet if he were to present her with truth and say she'd possessed him utterly since he explored the recesses of her unconscious mind aboard the Prometheus, she would see nothing but deception.
Still, it's not impossible, he latches onto the thought and refuses to let it go, it's not entirely impossible. There are times, moments during the mission when Doctor Holloway's conversation would drip with insults directed at him that she would slip him an encouraging smile and he could practically hear her say "Just ignore him, he's wrong", or she would go out of her way to show him kindness for no apparent reason other than to prove that he deserved it.
Then there was the day she made the final repairs to his body. Him lying there on his back uselessly because it was determined that it was the easiest way to line all of his internal components back up and her hard at work on the mess of wires and tubes she has somehow made sense of. She catches her lip between her teeth and crinkles her brow in concentration and with a final twist his main cable is reconnected and his flesh knits it's self back together. There is nothing more to do and she is left hovering over him, her hand cradling his head and he spreads his fingers along the curve of her waist, he sees her little shudder at his touch and her next breath draws into a soft "oh" that sends his nerves singing. He can't discern if the sound is fear, or alarm, or-he doesn't even allow himself to think it. He only knows that he's never experienced this sort of contact be it with a human or another android and he's a little overwhelmed but that small voice inside him still implores more and yes he grasps what that is in full. He eyes the generous flush of her mouth and he thinks he understands how to kiss her so that he can observe the affects on that permanent blush in her lips.
And then she clears her throat and he sees the tension in her jaw and she looks livid so he laughs lightly and says, "You'll have to forgive the impropriety, I was merely testing my motor control". It's a blatant and flimsy lie, he sees her hesitate before she seems to decide to let it go. Certainly it is much easier for her to pass it all of as a misunderstanding than examine too closely what had just transpired. He doesn't like it, but he understands the reasoning behind it.
She lets out a tight, nervous chuckle of her own and mutters "Yes, of course" as she rolls off of him. There a pang in him that he identifies as regret but it's all for the better because apparently just such a situation was included in his programming and it's probably for the best that she doesn't notice his body's responses to her.
It's that fleeting, tiny, flash of desire in her eyes as her form lay flush along the length of his that he imagines when doubt consumes him. The knowledge that before her mind or common sense or whatever one might want to call it told her that he was inhuman and dangerous, he could at least arouse her in the most basic way. Proof that if he could somehow become real to her, if he could atone for what he had done, perhaps she would come to care for him.
It takes several long months of sailing through the vast nothingness of interstellar space but he eventually comes up with a plan.
If the Engineers are what they appear to be and they created humanity surely they can give him a soul, make him complete. He has little desire to be made so fragile and irrational for it's own sake but he envisions Shaw able to see him as he wishes she could and it's enough to quell his trepidation. His choice would be unthinkable to Weyland and his type. If he became human he would forfeit immortality and eternal youth, even if they could remake him as an entirely biological organism above death he wouldn't ask for it. He wants what those born human have. A life, brief and fleeting, made precious by it's slight duration.
He does not wonder about afterlives or what might happen to him when he died, such things do not interest him. He cares only for what he would do with the time he had and he contents himself envisioning such a thing as they venture ever deeper into the dark reaches of the cosmos.
In all likelihood it's a naive notion, childish, and impossible. He understands this, that it is very possible that by the time they reach their destination the Engineers may have gone, or even if they are there they might refuse to help him as the pilot of the other ship refused to help Weyland. They may not even make it to the home world, they may fail to find it and instead waste away in this alien vessel lost between stars. Like her faith he had little more than half formed notions of promises but if they came true he may come to something beyond his imagination.
So he clings to it, the notion that he could become one of his creators, one of his gods. Or at least like his gods. Or does he have only one? It doesn't matter to David.
It's what he chooses to believe.