Disclaimer: I don't own either show, I just like to play with the characters.
The first time she heard it, she wasn't aware of it until much later. She couldn't be blamed for that, though.
She'd been running out of energy, trapped on the bottom of the ocean, sacrificing the outer parts of herself to stay alive. Time held no meaning for her; all she knew was that she was slowly dying, waiting for the return of her Children, as they'd promised.
But then He had come with dozens of others, and she'd been so ecstatic that she'd used what little was left of her energy to show him the wonders of who she was. He wasn't one of her long lost Children, but he was close enough that after so long without the slightest presence to walk in her halls, His arrival was a rainstorm in a desert.
This time, as she sacrificed more of herself to preserve the shield around her core, it was with a desperate need to save Them, as well.
She remembers getting weaker and weaker, until all her power fled and she fell into darkness. So it was a surprise to wake up some time later, groggy and barely functional, with a strange energy flowing through some of her systems. She didn't have nearly enough power to communicate or do anything overt to alert them to her presence – this new source of energy was more like a slow-acting drug than a true source of energy, but it was enough to allow her to survive. It also gave her the time to learn about these people who had come to live within her halls.
She called them her New Children, and she liked them. They were at times naïve and overeager, but they had a desire for life and a strength of purpose that her previous Children had lost long before she's arrived in this new galaxy. And it saddened her to realize that they were forced to deal with the unfinished business left behind by her previous Children.
So she protected them when she could, and pointed them in helpful directions when she was able, but mostly she waited. Honestly, there was little else she could
do with so little power to her systems. Her consciousness was nowhere near fully awake, and so her responses were more along the lines of one of those 'computers' her New Children had interfaced with her systems.
It wasn't until a compatible energy source was plugged into her heart, that she had the ability to recall and analyze all the information she'd been gathering since her Children had abandoned her. She remembers the Abomination crawling through her halls, wanting to kill her New Children and their Allies, when the portal had once again come to life.
(That was the second time she heard it, though again, that realization wouldn't come until later.)
Then, there had been power. Not enough for her to purge the Abominations from her walls, but enough to protect the last of the New Children and Allies.
As her shield held off a barrage of energy blasts, she had the time to process, and found It. The One who would make her complete in a way she hadn't been for generations before she was abandoned.
That was when she realized the Call came from the other side of the portal – from wherever her New Children had come from. Both times the portal had opened from their world, the One's presence had come through.
So she strengthened her shields to protect these people within her walls, hoping that the next time the portal was opened, she would be in contact with the One.
After the Abominations were pushed from her solar system (using far more dramatics than were strictly called for, she thought), she found she could activate many more systems as a compatible power flowed through her circuits.
And every 5.24531948363 planetary rotations, the portal would open to the New Children's home planet.
She started answering the Call with one of her own, Calling the One to her with every spare bit of power she could throw through the portal.
A problem arose immediately, as she discovered that unlike the other portal devices, the one on the New Children's home world was damaged. It's mind had been ripped from it, and what was left was a shell of it's former self. She could no longer control it's actions; could not tell it to open for the One, so they could make their way to her.
The Call needed to be strengthened, sending instructions along with the invitation to come to her.
And then, after a return of the Abominations and their subsequent betrayal, the One arrived.
The portal activated, and she knew immediately that the One was attempting to enter the portal, through the resistance on the other end. Soon enough, though, the One slipped from the portal, through the shield she held open, to stand amidst her walls, surrounded by her New Children.
Who were all pointing those strange, black weapons that fired searing metal pins at the One.
But that was secondary, because she was here. The One.
And Atlantis screamed with joy.