The girl in the cage draws his attention for a number of reasons. Or, rather, she keeps it for a number of reasons—the very first being that, had she not leant toward him so suddenly, he wouldn't have noticed her at all.
His first instinct is to keep walking. Years of keeping his head down means ignoring any suspicious prisoners or pathetic beggars, lest he put himself in the spotlight. But years of being Arthur's manservant (and years of saving his life in increasingly conspicuous and risky ways) has beat that instinct down just enough for him to do a double take. Just enough for him to notice the weak trickle of magic that flows from her.
This wouldn't be alarming if Merlin's ability to sense others' magic hasn't been the only thing that's kept him and Arthur alive on many occasions. It's not a conscious thing—Merlin's magic does it independently, stretching out languidly into the air and earth around him, giving him a little taste of everything. Not that he's particularly conscious of it; to him, it's as unobtrusive as the weight of his clothes. A man dry of magic would be alarmed at the potency of sensation that Merlin feels. In fact, a sorcerer would probably be alarmed as well—Emrys is, after all, much more potent a magic user than any others who walk the earth.
This aura of magic that surrounds Merlin is very good at recognizing when foreign magic mingles with it. It's a built-in alarm system, and the fact that the girl in the cage didn't ping it is momentarily terrifying to Merlin. That a sorcerer could hide from him is an awful, horrific thought when, in countless numbers of his exploits, he has only just caught an enemy in time.
But the next thing that keeps his attention is that he realizes she is not hiding from him by intention. No; this girl is in rags and mud cakes her skin. She would not have the strength to suppress her magic so deeply, and, judging by the look in her eyes, she would not have the will to do so, either. She must have just the barest trace of sorcery in her.
Despite how little magic she must have, the last reason Merlin is captivated by her is simply the fact that she is of magic. That she is a druid, and she must be in this cage because of it. Merlin, starved of interaction with magic that is not tainted with malevolence, finds himself with a sudden, desperate longing to know her.
So he stands there looking at her just long enough to let the pity latch on, and he knows even as Gaius coaxes him away that he won't leave her there.
Human infants, even if fed and bathed, will die if they are not cradled—if they are not held and touched and cooed at lovingly. Humans are social creatures, and even in adulthood the skin will hunger for embrace and for affection if it is avoided for too long. A person will itch for companionship.
In the same way, a sorcerer's innate magic will long to mingle with other magic—magic unique to other sorcerers or the latent magic of the Earth and its creatures. Normally this is less of an issue than skin hunger; magic is everywhere, and as shown by the druids, magical people tend to flock together.
For Merlin, it's not that simple. In Ealdor, he was the only sorcerer for miles, and the Earth was his only source of comfort. Not a significant loss by any means—sorcerers were always meant to be small in population—but when Merlin went to Camelot, had he been conscious of it, he would have noticed that even the planet was barren of magic there.
The absolute extinction of sorcery in Camelot was not exclusively a material loss. Magic users were executed, certainly, and their magic disseminated back to the natural world. But what followed the banishment of magic and the executions and the witch hunts was a culture, a mindset, a thought that spread through the kingdom like a plague: magic is evil. What followed was: magic has no place here.
And the thing about magic that has not attached itself to an individual is that it is more intelligent and—quite tragically—more kind than any living creature. So it listened.
Magic left Camelot, leeched from the earth and sky down to the core of the planet. For it, the trees grew just a little less green and the sunsets fell just a little less vibrant and the deer had just a little fewer fawns in the spring. For the most part, however, little changed in the active lives of people. And as such, when Merlin came to Camelot, conscious or not, his magic soon grew to hunger for an embrace the way his skin did. His skin could be assuaged with Gaius' rare hugs or Gwen's affectionate gestures—even once in a very, very long while by Arthur's brotherly embraces—but his magic could not be quelled by any of that.
The closest he ever comes is to the magic of sorcerers who enter Camelot solely to cause unrest, but that doesn't count, not really. It is as little comfort to Merlin's magic as a hand around the throat is to the skin.
For both Merlin's magic, unknown to his conscious mind, and his conscious desire to be around others like him—well.
The girl in the cage is like a beacon. Like a sun.
It's hardly difficult to predict that Merlin would free her the next night.
Merlin does not know that Freya is cursed, in the beginning. He does not know that the bastet is the reason her magic is so thoroughly repressed. All he knows in the beginning is his strange, desperate desire to be close to her—to hold her and make her happy and make her laugh. He takes it for love, as humans would. It is not love, not really, but.
It might as well be.
If Freya were to live, and the bastet were to calm or to leave her, and if she and Merlin were to build a home by a lake by some fields with some cows by some mountains, they probably would fall in love for real. It is definitely a puppy crush that makes Freya lie and say yes to Merlin when he asks her to run away with him (she lived with the druids before, you'll remember, and even if they were afraid of her curse at least they were there. At least their magic flowed around her. So she isn't parched like Merlin is. She isn't dying of it).
But Merlin is ravenous, whether he knows it or not, and what he takes for love is in fact a desperate hunger. Her sweet little hint of magic makes him tingle like the skin does when someone sits next to you and their leg touches yours.
What makes Merlin kiss her is that the hunger is too much, too horrible, and she is a tease whether she knows it or not and his kiss is an attempt to get at what dwells in her. The only thing that keeps the kiss so sweet is his own self-control. He doesn't want to scare her off. He doesn't want to lose her. He can't lose her, actually, he'll die if he does and he'll die before he lets her be found. (And what makes Merlin kiss her, a secondary thing, is the grief that lies latent and constant within him. He grieves for his isolation, for his lies, for that he is a warlock imprisoned by destiny, bound to a man who would have him dead in the beginning and who won't be able to accept him until the very, very end. What makes Merlin kiss her is that the loneliness is too much, too horrible, and she is like a lifeline. She is like a sun, and everything that keeps the kiss so sweet is that he wants her, at least, to know something gentle. To know something kind. He tells her that magic can be good and he conjures her a little rose in place of a strawberry and with his lips he tries desperately to let her know that there is kindness in magic, there is, there has to be, and it's a little bit of a lie. Merlin has had to find that goodness for himself, you know. To him, magic had always seemed so tragically unkind.)
But Freya will be found, and Merlin will lose her, for she is the bastet. She's killed two civilians and two castle guards and will die by the sword of Prince Arthur Pendragon, and in the end she will not blame him. It is Camelot or her and she never wanted to hurt its people. Merlin will not think to blame him either, especially not later when he very unsubtly makes an effort to cheer Merlin up.
Merlin's magic will yearn for Freya, though, and it might as well be his heart for the way he carries her to her place of rest. It is that yearning that will make him cry, feeling her magic return to the earth as her life fades. When she tells him he saved her, he made her feel loved, it will be his real heart (the one that grieves) that breaks a little.
And when Merlin sets her afloat on a lake by some fields with some cows by some mountains, it is his heart that will cause him to hesitate before he sets her aflame.
In the end, Merlin will not be in love with Freya while she lives. But he might as well be, really, because his magic will twist around her and in her like vines, like loving, drawing them together and bringing tears to his eyes and gratitude to hers. He might as well be, really, because he is magic and magic was what needed her so desperately.
In the end, what will make Merlin visit the lake time and time again, what will have him entrust Excalibur to her care, entrust Arthur, will be love. A posthumous love, but love nonetheless, for by then his magic will have forgotten her tease, and even by then, his heart will remember, fiercely, her beauty.