I decided to put the Alternate Ending idea i had as a epilogue. Please enjoy it.
Lyra watched as the Human walked through the portal back to his world and it took all her strength not to jump in after him. Once the portal had collapsed she reached into her saddle bag and pulled out a large bag of bits putting it on the table.
“2000 bits as agreed. Now hand it over.” She said turning to face Celestia.
“Alright.” The Day Monarch said levitating the medical cup over to her and tucking the bag of bits under her wing.
“Mmm.” The Mint Green Unicorn moaned licking some of the sperm.
“Um Lyra. You better hurry. The operation is in half an hour.” Twilight said looking over at a clock.
“Oh Right!” Lyra said running out of the Library and down the road to the hospital.
Lyra woke up 2 hours later in a hospital bed her lover Bon Bon as well as Twilight and Celestia were sitting by the bed.
“Did it work?” She asked looking at all of them.
“Yes.” Celestia nodded. “You now have a baby Hoomin-“
“Human.” Lyra corrected.
“Growing inside you.” The alicorn finished unfazed by the correction.
“Isn't that great Bon Bon?” The green Unicorn asked the Cream coloured Earth Pony mare. “Soon we’ll be the proud parents of a baby Human.”
Tears of Joy ran down both mares cheeks as the hugged each other, happy for their unborn child.