Years after Twilight baptized Scootaloo Twilight was sitting at her map table in her castle trying to look for a ripped page in her book as she wanted to fix it.
She couldnt remember who ripped it but once she did fix it she realized she had dine it by accident.
After she put the book away Rarity entered the castle and walked up to Twilight.
"Twilight there you are I was looking for you." Rarity said. Twilight stood up and went to meet Rarity.
"What do you need Rarity?" Twilight asked as she asked the fashionista.
"Pastor Amy has asked me to ask you to come to church for sacrament Sunday." Rarity said.
"Why couldn't she just ask me directly? Besides I'll be there anyway but I will be a bit late as I'll be visiting Canterlot that morning." Twilight said.
"You didnt tell me you were doing that." Rarity said, Twilight shrugged.
"Sorry, Im...seeing Celestia...for a meeting...." Twilight said slowly.
"Well you dont have to go if you dont want to but Amy asked for you to be their I dont know what she wants but it sounds important." Rarity explained.
"She wants me to be there huh? Alright I'll be there but your going to have to tell her that I wont be there till later." Twilight said. Rarity nodded and left.
Soon a week passed and Twilight went to the service in the church at Ponyville and paid attention to it. When she was done she went to find Amy. Soon she found her.
"Amy! I heard you needed to speak with me?" Twilight said.
"Yes. I presume Rarity got the message to you then?" Amy asked as they tried to hear eachother over the crowd.
"Yes she did, let's go somewhere where it's easier to hear eachother talk." Twilight said. Amy nodded and led her to the hallway that led to the church kitchen she closed the door and turned to Twilight.
"Amy what's wrong? I heard from Rarity that it was probably important. Do you need help with anything?" Twilight said, Amy looked at Twilight with fear in her eyes, Twilight could tell that Amy was scared.
"Twilight...theres something I've been trying to tell you for the past few services now....but I never had the courage to do it." Amy said with hesitation.
Twilight wanted to help Amy tell her as she could tell that something was bothering Amy so she wanted to help her.
"Its alright Amy you can tell me anything, I'll help you like how a sister in christ should." Twilight said reassuringly. Amy stopped and closed her eyes and took a deep breath than exhaled to calm herself and then she spoke.
"Twilight I'm resigning from my pastor position...I'm leaving the church." Amy said. This came as a shock to Twilight, Twilight had not been expecting Amy to say this to her.
"What?! But your my favorite you cant leave!! Why are you leaving!?" Twilight said as she got upset. Amy frowned.
"I know Twilight. Your such a sweet girl and I'm grateful for you being a princess. I'm glad I had the honor of baptizing you but I cant stay this was my last day here. I'll give you my new phone number right now if you give me a second." Amy said. Twilight nodded and Amy wrote it down. Amy then gave it to Twilight.
"Amy why are you leaving I dont understand!" Twilight said as began to sob, Amy sighed and pulled Twilight into a hug and Twilight let her tears fall down her cheeks. Twilight began to sob.
"Sssssshhhh! Its okay its okay." Amy said. Twilight held on to her pastor tightly, not wanting to let go finally she had to.
"Why are you leaving!? Please I must know!" Twilight begged. Amy began to say something but a voice interrupted them.
"Let's go Amy!!!" An angry voice yelled. Amy shook with fright.
"Amy your shaking like a leaf..." Twilight pointed out with a concerned tone. Amy just held on to Twilight as she didnt respond.
Twilight wanted to know about what was going on with Amy and why she was so scared and who that voice was.
"Amy please tell me what's wrong..." Twilight said but Amy just hugged her even tighter.
"Amy come on right now!!!" The voice shouted angrily. Twilight looked at the door as she began to get scared herself.
"Amy..." Twilight began to say but Amy removed herself from the hug and shook her head.
"I'm so sorry Twilight." Amy said and with that she left the room and the man took her by the arm and dragged her out roughly.
Twilight stared at the scene in shock she wanted to yell at the man and defend Amy but knew that she couldnt do that as it would cause a commotion in the church.
Fortunately for Twilight the church goers shared Twilight's same exact shock as they watched in confusion as Amy was lead away forcefully.
Twilight stood there wondering why Amy had been so scared and why she had been treated badly.
Twilight left the church and went back to her castle in Ponyville while she continued to think about Amy.
Twilight didnt hear from Amy for several days so she got worried for her. She started to pray for Amy everyday when she didnt hear from her.
As Twilight went about her schedule she would check to see I'd she got any letters from Amy explaining why she had been treated badly and that she was okay.
One of the days Twilight went back to the church and asked about Amy but several pastors told her that they didnt know either.
Twilight then waited for the next Sunday to see if she got an explanation for what had happened but they all told her that they didnt know.
Twilighy became scared for Amy as she wondered if something bad had happened. She even went Canterlot and filed a report about Amy. Celestia was so nice to take up an investigation on whay had happened to Amy.
Twilight waited for the results to come back to her. As she waited for several days she stopped paying attention to the time.
One day when Twilight was waiting for the results in her own castle Rarity came up to her and spoke to her.
"I know how you feel about Amy Twilight I'm sure she will respond to your letter." Rarity said. Twilight just nodded.
Soon after a month of waiting Amy finally wrote back to her and sent her a letter, Spike handed it to Twilight the at the second he had seen the name on the envelope he knew how distraught Twilight had been waiting for Amy.
When Twilight opened it up she read what she had not been looking forward to.
Dear Twilight,
I'm sorry it took me a while to get back to you but things have been tough for me, I apologize that you had to witness that scary event happen at church I was not expecting to be dragged our like that.
I'm sorry for not giving you a better explanation that day but I couldnt as I didbt want to make my family angry. That was my father that you saw....
Twilight this might come as a shock to you but...I'm gay....that's the reason why I was pulled from church. My family has deemed me a degenerate and has locked me in my room until they can get me the said treatment that can supposedly turn me straight.
I'm so sorry Twilight. I hope your life doesnt suck like mine does.
Love,
Amy"
Twilight dropped the letter and cried profusely. It all made sense to her now, she realized the reason why she had been pulled out from being a pastor.
"Twilight what's wrong?" Spike asked her as he walked up, Twilight showed him the letter and he reacted with disgust.
"I hate intolerant christians." Spike muttered. Spike softened his expression.
"I'm sorry for that happening Twilight. You must have cared about you alot." He said. Twilight nodded as she sobbed.
"She b-baptised me and everything! I'm so worried about her!" Twilight cried. Spike frowned.
"I know." Spike said softly.
"Why do you care though...your an athiest." Twilight sobbed.
"I'm an atheist yes but I do care about what happens to human beings. I hate what Amy is going through. These judgemental christian's have always made the religion look disgusting to me...sorry! Its you got me mad now." Spike said.
"Its alright Im so scared for her." Twilight sobbed. Spike nodded.
"I understand that, I really hope your friend gets away from her fucktard family. Hate like that doesnt belong in Equestria." Spike said. Twilight nodded. As Spike held her she soon calmed down.
"Its alright Twilight she will pull through. I'm rooting for her." Spike said.
"Thank you Spike." Twilight said. They stopped hugging and Twilight went to her room to calm down. A few weeks later Amy wrote another letter to Twilight saying that she had escaped from her bigoted family and had gotten a house by herself and that was now preaching in a more accepting church. Twilight started to going to that church and her and Amy celebrated Amy's freedom.