There are many rules when it comes to Time Lords.

Respecting elders and following orders are some of the rules that Galliferyians must obey, but only when it comes to breeding do the rules change.

There are ranks within the Time Lords that are not spoken upon but rather known by instinct when born. Each Time Lord gives off a certain scent that indicates what rank he or she holds; Alpha, Beta, or Omega.

The Alphas are the stronger, more powerful ones and holds a higher rank than others. They are dominating and territorial when it comes to their mates and can be very aggressive and possessive when their mate is in heat. Their first priority is to make sure that their mate/partner or family is safe under their protection. Alphas only mate with Omegas and when they do they rely only on instinct which is to fill his Omega's needs by knotting and impregnating her. The Alpha knots when both partners are on the verge of orgasm and the base of his cock swells up, preventing him from pulling out and pouring all of his seed into his female, impregnating her. Knotting only occurs when both mates are bonding during heat, once the Alpha Male knots then they are mates for life. An Alpha holds a lot of semen to ensure that his female is pregnant during heat, if the Alpha does not join his Omega in heat then she will go through that period of intense pain and arousal until it's over(which may take from a few days to weeks). Time Lords, especially Alphas, can immediately smell when their mate is in heat and can mark them by rubbing their scent on them or biting them. Alphas do not and cannot mate with Betas.

The Betas are like your normal everyday people who do regular people things. Betas don't mate with either Alphas or Omegas simply because they can't. It's against the rules for a Beta to mate especially with an Omega, they first must be of a higher ranking(Alpha). If a Beta were to mate with an Omega(or an Alpha) they would be shunned and thrown down to the rank of Omega.

The Omegas are the lowest of the low in the ranks and are looked down upon. They are usually submissive to anyone of higher rank and are genuinely caring. They periodically go into heat and they can't go through it alone without an Alpha to fulfill her needs. An Omega can get pregnant and can bear children only from an Alpha, not a Beta. For a bond to be complete, the Omega must agree to the relationship she has with her mate and participate in the mating process. The Omega must always be submissive towards her mate whether it's during heat or not simply because it's part of their DNA and instinct to submit in any way.

The Doctor couldn't help by thinking of these ancient rules as he carried Clara out of his time stream and into the dead TARDIS. While he was searching for her in his God forsaken tomb, he had managed to catch the scent he thought he would never smell again. The scent of a Time Lady. An Omega Time Lady. He had tilted his head back in the air and sniffed. And she was fertile. He had felt his body react to such a scent but quickly refocused on finding and saving Clara, but he found that as he drew nearer to her the scent grew stronger and it caused his instincts surface. The Doctor knew that the scent shouldn't affect him this strongly but he hasn't smelled it in over hundreds years and it was making him very hungry for touch and intimacy. The Doctor isn't sure how Clara could've picked up the scent of a Time Lady, but he pushed the thoughts down along with his instincts and quickly gathered her up, leaving his time stream and his greatest secret behind.

As soon as he stumbled out, Vastra, Jenny, and Strax were there to help him back to his TARDIS. Strax had offered to carry Clara for him but the Doctor declined, clutching her closer and inhaling her scent. During their journey back, the Doctor had thought how it was possible that Clara had picked up the alluring smell of a Time Lady even when she is one hundred percent human. At least she was the last time he'd checked. Unless one of her echoes landed on Gallifrey. No, he thought, it's not possible. It couldn't be yet here she was in his arms, his nose practically buried in her neck.

Once they stumbled into the TARDIS, the Doctor immediately set the coordinates for the three detectives' home, still not letting go of Clara making the process much more difficult. Vastra and Jenny offered to help many times but the Doctor refused, telling them they should head home before another disaster occurs, no pun intended. They all left reluctantly leaving the Doctor to steer the TARDIS into space and to carry Clara into his bedroom where he laid her down, pulled the covers over her and sat next to her on a chair he grabbed from the corner. All the while pondering over the idea of Clara as a Time Lady. He watched as her chest moved up and down and how her eyes moved under their lids, he caught a rebellious strand of hair and softly pushed it behind her ear. He leaned forward and inhaled deeply, humming in content at her scent.

He then laid an arm around her waist, pulling her closer to him. He flipped out the Sonic and scanned her body before reading the results: Time Lady. The Doctor's eyes widened and looked down at his impossible girl who has been ripped to a thousand shreds, echoes of her dying over and over again just for him. He owes her everything now. But he still can't believe it. Clara, his Clara, a Time Lady. She has seen everything he has done, knows about his darkest days, the things he had done that he wishes he could take back. And now she has seen his planet, his home. She has lived a life there with him, even though he doesn't remember seeing her. Oh, Clara, my Clara, he thought, Mine.

His head shot up. Did he just say Clara was his? No, Clara wasn't his. She was never his. But his instincts thought differently as he caught some more of her scent in his nose which triggered a part of his brain that let out the Alpha in him. No. Must not let it out. Clara literally just got back from dying a thousand times you can't just claim her like that! Yes, you can. No! Yes, do it, you're an Alpha you can claim and Omega like her. No! Stop!

The Doctor shook his head to get the thoughts out of his head. He would not let his instincts get the better of him.

As he rests his head against her chest and breathes in her scent, he vows he will do whatever it takes to make his Impossible Girl safe under his protection.