Ruby dragged everyone back to the throne room (She ousted the ruler at the time and became queen), and she wanted to use them to help her seize power. As you expect, the humans did not agree to her plan, so she was forced to take it the hard way: brainwashing every last human to fight for human kind. She put her parents as the co-leaders, while the others are also at a very high rank up on the army.
Just in case anyone here forgot , the major combatants of this war for the human race are Ruby Red as the captain, with the Dreemur couple, and the gaming group are pulled into this one as well.
Meanwhile, on the pony side, Sapphire overthrew Celestia and forced her to pass down the crown to him. He again, brainwashed all the ponies and forced them to fight for ponykind. There was obviously the mane seven, the princesses and the captain as the major ones of the pony race. And just because he's married to Twilight, Nathan also went to join the ponies.
The worlds were so different when the second pony war took place. In the first one, Zebulon forced all countries to attack, but this time, both sides showed no mercy against the other tribe, and anyone who tries to disobey will easily be executed. Surprisingly, unlike the first war, this time both sides were completely at an impasse.
The first battle sparked in the United States.
'Listen up, people,' Ruby said in a serious voice to the army. 'We all know here that the ponies will be destroyed in this war. We shall show no mercy to them this time! We know peace is nothing but an excuse to stop fighting. Peace is a thing that makes us weak. Mercy is no solution to stopping this war. And we will not stop until one side falls, and that will be the ponies. Do you hear me!?'
'Yes, captain Ruby!' Everyone replied.
Soon, the ponies came, with Nathan riding Sapphire into battle.
'They're here already?' She chuckled in her mind.
He got off the captain's back, and the two and the whole army were ready for the first battle of the second pony war.
'Alright, Everypony. It has all come down to this war. Every battle counts, we will not stop fighting those humans until they suffer defeat! Anyone of you who betrays our kind, you're going to have a bad time... You hear me, Everypony!?' Sapphire demanded.
'Sir yes sir! We want war!' Everyone chanted.
'Then what are we waiting for!?' Nathan yelled. 'Viva la Equestria!'
Ruby wasn't ready to lose on them either.
'No mercy! Charge, my fellow humans!' She yelled back.
Both sides clashed at the center of the open area. Looking over from the high ground, the two leaders flew into the air, drawing their swords as they got close.
'Let's settle the debate, for real this time!' Sapphire shouted.
Ruby laughed. 'Don't fret, my opponent. When you guys die... you all will meet again... In hell!'
Both of them clashed their swords angrily.
The war continued for the next 5 years, with both sides showing no mercy. Thankfully, the group of humans and the ponies managed to secretly keep in touch. The two didn't notice at first that their spell for some reason had a major flaw. As these particular humans and ponies were dubbed the legends of the two kinds, it was not powerful enough to completely brainwash their minds. It will only respond when they were in battle. When they're not, it disables.
The two leaders didn't disable social media for some reason, so the groups tried to help each other to crack the mystery of how these two broke apart. They suspected it had something to do with their souls and there was a spell controlling them, but they weren't sure.
One day, they were texting on their phone.
'Hey... Frisk, it's been quite a while.' Twilight texted.
Frisk was really depressed. 'I know, Twilly. I miss you guys. We all miss the ponies.'
On the other side, the gamers were discussing in their own chat group how they will get out of this hell. They had to text each other from time to time since they sometimes were in different countries and the portals have been disabled in case the ponies use them to travel from place to place faster.
'Guys, we really need to find some way of getting out of here.' Mark said.
'This spell, though... I hate it, every time we go into battle, it just controls us and we can't fight back!' Stacy was worried.
Dan wondered a little bit. 'There must be some way to break the spell we have right now, we should turn to our pony friends for help soon.'
As Joseph was about to text another message, he got a phone call from someone.
'(Sigh) Why would anyone call me at this kind of time, though?' He sighed, answering the call. 'Hello, this is Joseph, who's this?'
The caller from the other side was relieved. 'Hey... Joseph, I'm glad you're okay right now.'
He realised who she was. 'Oh, Bethany! How's it going?'
Bethany used to be his best friend, but since the second war started, they lost touch.
'I heard that you and your pony friends have separated, are you alright? By the way, I know you guys have a spell inside your heads right now and you can turn on me if I say this... I have a plan, and I need your help.' She explained.
'Yes, I'm fine. But... What's your plan? We don't even know what's causing those two to fight all of a sudden!' He replied. 'And also, are you trying to betray our kind? You don't stand a chance!'
'Listen to me,' She said calmly. 'I know exactly what happened to them. It's their souls. Their souls were replaced. They aren't themselves anymore.'
Joseph gasped. 'I knew it! But... How did you know?'
'One day, I randomly picked up a red coloured soul that landed while I was resting at the park. It seemed like something special, so I kept it to myself and never told anyone about it. However, when the war started, I knew there must be something wrong. I decided to see if I can figure out the identity of who this soul belonged to through secret experiments that only I knew about.' Bethany explained.
'And what's the result?' Joseph asked hurriedly.
'It gave me a girl, named Astell Dreemur.'
He had a big gasp. 'What!? Do you not know who that is!?'
'Who is it?' She asked.
He was speechless and went silent.
'Hello? Are you there?'
An idea immediately clicked in his head. 'Aha! Thanks Beth, you gave me so much help! Alright, I don't have much time. Keep in touch with me, I'll tell you what to do if I decide this plan will work. Bye for now!' He hung up the call quickly.
'Oh my word, did she actually pick up her soul? I ought to tell the others about her plan!' Joseph thought, texting on his phone.
Frisk just received the text from him.
'Interesting... His friend had a plan? Well, we need all the help we can get!' She thought.
While she was texting on her phone to ask the others, Ruby came in.
'Hold on... Mom, what are you doing?' She asked.
Frisk immediately turned off her phone. 'Nothing! Nothing at all!'
Ruby came close to look her phone. 'Are you texting to your friends?' She took the phone away.
'Oh, someone kill me...' Frisk thought.
'You're betraying me!?' Ruby yelled at her. 'Guards! Get this traitor out of my sight!'
They came in quickly and took her away.
'You little cheater... Soon, your friends will be punished as well...'
The next day, the others were accused of betrayal quickly. They were all going to be executed one day after they were discovered.
Meanwhile, on the pony side, the mane seven were trying to find ways to disable the spell completely.
'There must be something we can do...' Flurry Heart thought.
'I don't know, even with my knowledge, I can't find a way to disable it!' Starlight replied.
Rainbow came over, feeling unamused. 'If only Frisk came back, we would've prevailed just like how we did in the first war!'
'Do you have any ideas, Tia?' Luna asked her sister.
'I'm afraid not, even this kind of magic is beyond our understanding... How could he be so powerful?' She said.
Suddenly, they heard the sounds of a pony crying.
'(Sigh) I feel so sorry for Twilight...' Cadance said.
In her room, Twilight Sparkle was crying so many tears.
'(Sobs) Lunar... Why... (sobs) Why do you have to do this? I loved you with all of my heart...' She cried.
Peeking from the beyond the door, Nathan was really depressed too. He wanted to comfort his wife really badly.
'Do you need anything, Twilight?' He asked.
She lightly turned to him and shook her head. 'No, thanks. Just... (sniff) leave me alone for a bit...'
Nathan felt a tear rolling down his face. 'Twilight, you can tell me about your feelings. I don't mind.'
'How could he have betrayed us?' She asked herself. 'He was our son... And something took him away from us... It must be Ruby. We won't show mercy for this one, not like me and Frisk. We'll stand to the very end of the war this time around. Even if she's my best friend... Even if we humans and ponies used to be friends... I will not stop until I can get my child back.'
He was shocked. He never thought she'll say that.
'Sweetheart...' He said, walking to her.
As she closed her eyes to cry again, she felt a very warm and comforting embrace.
'Listen to me, Twilly. I don't want to hear you say that again... We all are one big family, humans and ponies, together. Friendship prevails, right? War will do us no good at all. The way we won last time is because you and Frisk agreed to reunite with each other. Then, it was then we worked together and brought peace.' He told her kindly. 'Our differences will never break us apart, as long we can work past it. You used to be a legend, a saviour of the ponies. After we married, and the other two, Asriel and me also became legends thanks to our help in the war. We will go back to the days of us saving everyone. I promise.'
She was still stuttering from her tears. 'Nathan...'
'I really mean it. Believe in me and yourself. Together, with harmony, we can stop this war by those childish adults who are nothing but a empty soul inside.' He smiled.
She finally dried her tears, and smiled. 'Promise?'
Nathan hugged her closely. 'Of course.'
Suddenly, princess Celestia came in.
'You might want to see what we found recently...' She said.
When they came into the throne room, they saw a magical chest.
'What's inside?' Nathan asked.
Luna grinned. 'I think this may mean something... Open it and see.'
Twilight opened the chest, to discover a pure, blue soul sitting inside.
'This looks strikingly familiar...' She said.
Flurry nodded. 'I found it a few days ago. It seemed it was the soul of Lunar Sparkle... We have to run some experiments to be sure.'
Everyone thought of the same idea.
'Twilight, this is our only hope.' He clutched the soul tightly in his hand. 'We need this... It will lead us the way to help those two.'
And for a certain period of time, the two groups did not have any contact at all. One because the humans were caught for betrayal, and for the ponies, they were busy analysing the soul. And the ponies didn't get caught because Sapphire was too busy on the war, he didn't notice.
Little did they know, the souls were their key to getting the two back together...