Explanations all around!

"... "Mother?"" Byleth asked, his stoic demeanor actually dropping. He had sheer shock written on his features. He glanced at Sothis, who just shrugged.

"...do you not recognize me, Mother?" Rhea asked, looking stunned, and even hurt. She then registered the harem outfit she was wearing. "And... what is that you're wearing?" Her Mother had never been shy with her body, but this was more than she remembered!

"Hmmm... Nope. Don't even remember anything from before I started waking up more often in Master's head... and no, he wasn't kidding about me being horny... It's a long story that involves a Lamp, and me becoming a genie essentially," Sothis explained.

"A... genie?" Rhea stared, trying to make sense of what was happening. "What even is that?"

"Well... it's like this..." Sothis began to explain, taking several minutes to sum up what happened, and what came of it. "...so yeah, I'm basically sexually liberated, submissive to Master, and really enjoying it!"

"..." Rhea was... drawing a blank on how to respond to this. It was just so surreal. After a moment, she decided, "I'm just... going to pretend not to even know about my Mother being a common whore to her vessel..."

"Hey! I'm no common whore!" Sothis puffed out her cheeks and crossed her arm. "I'm an extremely rare and valuable whore!" Of course the word "common" was what she took offense to. The sexually degrading word, she actually took pride in. Though, technically, she wasn't a whore, she gave her Master sex and more for free. But she liked being called that regardless. It was a Sex Genie thing. "Now, what's this about me being your mother? And what do you know about why I'm in Master's head?"

Rhea paused, and sighed. "The short version is that I... put your Heart within the chest of the Professor when he was born."

Byleth, who had watched passively, blinked at this. "...I'm sorry, what?"

"We are... a race of draconic beings. We can take human form, but our true nature is closer to that of Mother... we're called the Nabateans, the Children of the Goddess. My true name... is Seiros, the Saint who created the church so long ago, in the name of covering up much of the bloody history that resulted in your murder, and the murder of my fellow Nabateans... our Hearts, called Crest Stones, our bones, and our blood were plundered to empower unworthy people. You, Mother... were slain in your sleep by the despicable man called Nemesis... from your blood, he gained the Crest of Flames. From your bones, and your Heart... used to create the Sword of the Creator."

"...and, what happened to this Nemesis?" Sothis asked, going a bit green. To think, her original body was so thoroughly desecrated... even if she didn't remember it, she hoped Nemesis died painfully.

"I killed him myself," Rhea, or rather Seiros, replied. "I reclaimed the Sword of the Creator, and... I removed your Heart from it. I sought to bring you back, by any means I could... I tried many methods, using your Heart, and the one that bore the most fruit was by creating artificial humans to implant your Heart into. But none of them could awaken you. Then came Sitri, the twelfth. Even though she also failed to be a proper vessel, she was... special to me. I felt she was the one who came the closest. Then she fell in love with Jeralt, and soon became pregnant... with you, Professor. But your birth was complicated. In the end, it was a choice to save either you or Sitri. Sitri begged me to save you. I honored her wish, and removed Mother's Crest Stone from her, placing it in you to ensure you lived."

Byleth placed a hand on his chest. That... explained the whole medical anomaly of him not having a heartbeat, yet his blood flowed. He had a literal stone in his chest, which was moving his blood for his heart. "...and that's why Father left, isn't it? He had questions that he couldn't get answers to, and lost all trust in you for a while..."