Since after the United Global Alliance was established, Zero identity revealing to the world, and new colonized independent nation of CGSE, the world has changed for that time. Senba leaves the Black Knights to help Gen. Katase to rebuild the military and building the army for the next incoming Britannia invasion. The Black Knights become an independent organization to maintain peace for Japan and the world when they needed them and it was owned by Lelouch vi Britannia. With the help of Rakshata, working together with Llyod, they building a flying aerial cruiser for the Black Knights called Ikaruga.

The GDI that occupy Narita have set free and left Japan except Hokkaido to provide protection security with a permission from Prime Minister Ohgi. The Kyoto house have finally get their company back with full power of Japan and they continue gathering minerals for economy. The Ashford Academy was still a same as both Japanese and Britannian continue their schoolwork although they have to change the rules to strictly not allowed racism and discrimination in the school and provide security for protection. As for refugees rescued by GDI, they shipped back to Japan to live their reborn nation. The GDI helps them to reconstruct the ghettos for both homes and businesses. Chigusa aka Villeta Nu return to Japan from shelter, however, her memory return to normal self and see what happened to Area 11. At first, she attack both GDI and Japanese security team but Ohgi stopped her and explain everything to understand it. After the explanation, she was calmed down and then she had admit that she do love him even she has amnesia to fall in love with Eleven. Unfortunately, she had no memory of who's a shooter responsible of it. She stand his side until the end. Kaguya Sumeragi become a chairwoman of USJ, but later on, she'll join the Black Knights only to make Zero/Lelouch vi Britannian become her future husband.

Meanwhile in Euro-Britannia occupied Russia, the GDI forces under command of Admiral Alexei Bazarov engage the battle through the north to liberate Russia, and Alter-Russian militia force joins them as well to reclaim their homeland from Euro-Britannia. They able to take over some of the regions. Euro-Britannia have suffered losses of soldiers fighting against stronger army of GDI.

When broadcast was announced on live around the world, most of the Areas have rebelled inspired for Black Knights and UGA to take back their countries from Britannia oppression. Half of Areas have retaken their nations while some failed but they make resistance force to continue on the fight until they get their freedom back.

Heretic of Nod were remain hidden thanks to stealth technology to hide themselves from the world, especially GDI and CGSE.

The Australia Commonwealth economy grows larger as they possess the technology from GDI they provide it and to increase the economy. The Alter-Australians are happy to GDI to give them amazing technology they never invented before. They also have access the industry to gather more sakuradite for other purposes rather than war effort.

Henry returns to his new floating island as he became a colonial president of CGSE. The Tiber-Humans are happy to live in their new homes and they get a lot of jobs to support the colonized nation. Viktor become a general of GDI army, Jack Allen become a general of GDI air force, and Alexei become an admiral of GDI navy. Euphemia joins the GDI council member in time being before becoming new ruler of New Britannia. She will work as a chairwoman for political diplomatic to bring peace solution while Suzaku was still be her side. When they are not working, they went outside often to visit replica state of London and hang out together. What they didn't know is they both have feelings each other. Henry has ordered to sent all troops across the globe to liberate every country from Holy Britannian Empire.

Tom Smith has been promoted to captain for the battle of Japan liberation. The other has received promotions for their actions. Daniel Cruz was promoted to staff sergeant, James Wesker promoted to sergeant, Jacob Parker was promoted to Sergeant 1st class, Daichi Ito was still combat medic but he will be ranking to corporal, and Goro Azuma was promoted to warrant officer, which his siblings are happy to him.

Lelouch have visit to GDI POW prison to see Jeremiah when he had watched the broadcast on live, he wanted to give him a chance to be his side for he have failed to protect his mother, Lady Marianne. Lelouch accept his chance and Jeremiah become part of Black Knights and his bodyguard.

For Holy Britannian Empire, however, the invincibility of the empire is broken from Japan and other Areas liberation that they never aware of. The empire was humiliated and thanks to GDI and the allies, both EU and Chinese Federation are pushing back the forces from every land. France has retaken from Britannia and continue fighting them at the west side. The economy was crushed down due to USJ cut off the resource trading and GDI blockades the sea border at Pacific Ocean. The homeland becomes a battlefield as civil war erupts by Britannian rebel force made up of both commoners and military defectors. They were called Britannia Reformation Front (BRF), they are very loyal to Euphemia for kindness she give them and willing to fight against Britannian corrupt government. The royal family tried their best to maintain order but they failed as BRF rebels have seized one of the military base and used it against them. Charles was so furious of what happened to his own empire and he need to come up a plan to fix this problem. Most of the noblemen wanted to take back every Area they claimed to save their nobility and some who sympathize the rebels accept the remove of nobility and switch side to fight against tyrannical empire.

...

Heretic stormtroopers and militants found themselves inside the Scrin ship. They roaming in every room to secure the alien ship for themselves. The Elder, Jade, and Blood Vizier joins to look aroun the ship that has been here for a long time. As they walking around the room, Jade was looking on Scrin technology she can see to create a superweapon for the Heretic of Nod. She went up to Elder as she said.

Jade: Grandmaster, I have no idea the Scrin ship has been here the whole time without every one in this world notice it until we find it first.

Elder: People like Britannia are too forcus on "colonized" every territory on this alternate earth. They have no time to explore around except war and conquest. People's mind have no sense of it until there no one else to challenge their strength.

They continue exploring the ship when they enter the room to see there are few of chambers from both sides, and it became surprising because there are Scrin humanoids sleeping in each chambers for hundred years after crashing on this planet. Blood Vizier look around the chamber filled with sleeping Scrin humanoids to examine it then he said to his grandmaster.

Blood Vizier: Grandmaster, these things... they're alive.

Jade: Alive? How?

Elder: It doesn't matter. These will aid us for our goal.

Everyone in the room are staring him shockingly as he just said.

Jade: Grandmaster, with all due respect, these Scrin are the ones that almost destroying our earth and they see us as hostile beings.

Elder: They attack us because they think we resist them from taking our world as tiberium harvesting farm and we fight back. But since I have analyzed and study the body language of the Scrin, my communication to these beings is likely useful to our cause.

Jade was going to object his ideas but she won't dare to say a man who take her in as part of the family so she keep it herself. Elder walking around the chamber until he stumble upon a sleeping chamber different Scrin humanoid being from the others.

He find a control panel beside it so he press on it as the chamber door to release a Scrin humanoid being. It fell on the ground then he started to wake up and see that one who release him from his sleep chamber. Before it went to attack him, Elder spoke in alien language to him.

Elder (Scrin language): Halt. I'm no enemy of your Scrin.

??? (Scrin language): You spoke my language... Who are you?

Elder (Scrin language): I am known as The Elder, leader of Heretic of Nod.

Elder look at his men pointing guns at him until he order them to stand down to show that he's not a threat, not yet. He give an alien a hand. To response of Scrin alien creature, he grab his hand as he pulled him up to stand on their feet. Elder said to him.

Elder (Scrin language): What's your name?

??? (Scrin language): I am known as
Inanis.

Elder (Scrin language): Inanis... How would like to wake up your brethren. There's so much explanation to do. But right now, let's get business...

...

Zero was riding on his personal car as he drove to Ashford Academy. When he get there, he stopped the car and head out to visit his sister. He brought two personal guards to protect him from anyone attempting to take his life. As he walking towards his sister dorm, he notice there are students looking at him like he is famous person around him. He can heard them talking to each other.

Male Student 1: Hey! That's our Vice President of Ashford Academy.

Male Student 2: You mean him. Wow, we never knew he become a rebel leader.

Female Student 1: Quite a handsome, isn't it girls? He is a royal prince of Holy Britannian Empire.

Female Student 2: But I heard that he don't want to be a prince due to emperor send them here for exile.

Female Student 3: Nonetheless, he is handsome and quite a genius too.

He ignore their comments as he continue to toward the dorm until he encounter his friends, Shirley, Rivalz, and Nina blocking his way. Two BK guards stepped in as they said to them.

BK guard: Move aside. Zero has some business here.

Zero: That won't be all. I'll handle it.

Two BK guards back away as he goes in front of his friends. His best friend, Rivalz, just said to him.

Rivalz: L-Lelouch, is that really you?

Zero: You saying like you knew a person in front of you.

Rivalz: Of course, we are! I can't believe the most wanted person of Holy Britannian Empire happens to be my best friend and a royal prince too.

Shirley: Why? Why didn't you tell us you were Zero the whole time.

Zero: I don't have time to explanation as I come here to see my sister. But to your simple answer, the emperor, my own father, send me and my sister here for political hostage and invaded it without knowing we're here. Luckily for Ashford family like Milly take us in, we won't be here for a long time. Now please, excuse me.

Zero and his guards go through them and headed to the dorm. Then, he ordered his guards to stand behind and went to his sister dorm. Just before that, Milly was standing there waiting for his arrival and she said to him.

Milly: So... Lelouch, former Britannian prince become a most fearsome terrorist leader of the Black Knights. Quite a charming for a handsome man.

Zero: Milly Ashford...

He pulled out his mask to showing his face toward her as he make a smile and he said.

Lelouch: I would like to thank you.

Milly: For what?

Lelouch: For you and your family taking us in when we desperately need the most. You are the only people who loves my mother more than ever.

Milly: It's nice to hear that, Lelouch. But, may I ask you something?

Lelouch: Yes, you may.

Milly: I have feeling concern of what would happen if you were being caught in the battlefield and executed for high treason against your own country.

Lelouch: Milly...

Milly: No. It's not like I hate you for what you did. It just... it just that my whole life hanging with you and your sister ever since we were kids would happen in the future where I see you growing to become a revolutionary leader while your sister become a most gentle and kindest person she ever existence. I...

She feel shaking on her body as she tried to put up a smile on her face then her tears started to pour out of her eyes as she cannot control her emotions.

Milly: I would be depressing if something would happen to you. If you died, what would I tell your sister about your death? Would she'll be a same thing as me, feeling despair? Or, would she will be the next leader of the Black Knights and make her an enemy of the Britannia? I-I can't stand but feeling I will fail to protect you guys and I will be the most failure protector in the rest of my life. I-

Suddenly, he pulled her in and embraced around her body. He gently hugs her as he said.

Lelouch: Don't say that, Milly. You were the best person you ever be. You protect me and my sister from this desperate time. I look at you as my sister, Milly. And don't worry about me, I will always come back alive when I change the world for my Nunnally's wishes.

Milly: Y-You mean, you wanted her wish to be fome true?

He nodded.

Lelouch: Yes. A world would be gentle for Nunnally to live in. Once I change the world, you, me, my sister, and my friends will be enjoy without war and conquest.

Milly: Would be impossible, Lelouch?

Lelouch: It may be impossible. But with help of GDI and their allies, the world will be change forever.

Milly: Lelouch...

Lelouch: Hm?

Milly: Just promise me, promise me that you will come back alive to be with your sister, okay?

Lelouch: I promise.

They let go each other as Lelouch went in the room. Nunnally turn around to heard the footstep and then he said.

Lelouch: Nunnally...

Nunnally: Big brother? Is that you?

Lelouch: Yes, my sister. I'm here.

And with that, she rushed and hugs him tightly, and he did a same. They went to sit down at the table as they said.

Nunnally: Big brother, yesterday I watched on TV...

Lelouch: I know you seen it. I am Zero. And I have come here to see you, Nunnally.

Nunnally: Oh... But, may I ask. Why? Why would you become Zero?

Lelouch: To change the world the better for your wishes.

Nunnally: You wanted a gentler world as I wanted to wish for?

Lelouch: Yes. For you, my sister, I wanted the world where war is a history of the book and we can be enjoy our lives together. I wish you understand of what I did to change the world forever.

Nunnally: But, is there another way? Without violence? Is there a peaceful solution?

Lelouch: Nunnally, the world where people like our father despises everything for peace. People have discriminated to one and another person for different appearance. I do change it for good.

He place his hand on her shoulder as he said.

Lelouch: I promise you that your wishes will be fulfilled.

Nunnally: You promise?

Lelouch: Yes.

She feel unsure for her brother's action but he liberate the Japan along with his allies. So she replied his answer.

Nunnally: Okay. Just please, come back alive when it is over, okay?

Lelouch: I do.

He hugs his sister and head back to Black Knights HQ for working on the next move.

...

Euro-Britannia territory

GDI large army rushes through the field as they destroying enemy forces. Britannian liverpools firing upon them with gatling guns, cannons, and missile launcher to hold out the line but it is futile. The AMS fires ion cannons at enemy knightmares and push forward. The MG squad place down a position and fire upon britannian infantry force. GDI MARV fires sonic blasts at britannian sutherland and two zone railguns mounted at the right side of the tank fires at both sutherlands who are shooting at it. A squad of liberation knights slices through enemy forces using swords and guns. The britannian has no choice but to retreat.

G-1 base

A britannian commander was furious after seeing his forces are no match against GDI superiority forces.

Britannian officer 1: Sir! Our forces are heavily casualties and went to retreat.

Britannian officer 2: Your orders, sir!

Britannian commander: Retreat. We'll regroup and fight on again!

The G-1 base and his forces went to full retreat for a failure to push back the enemy.

...

GDI Russia HQ

Alexei was looking on the report that euro-britannian forces have full retreat to regroup. He able to take every region of Russia map to almost reaching the liberation.

Alexei: Hahaha! These imperial Britannians have finally afraid of the fury of the motherland. Ah, it feels so good.

Then, a personnel come to his office and he said.

GDI personnel: Sir!

Alexei: Ah, comrade. What is it?

GDI personnel: We've brought four people claim to be part of EU special division, the WZERO.

Alexei: Ah, yes. Bring them here.

A personnel went out to bring them here. The door opens to see four members of WZERO come to his room. One of them is Leila Malcal leading her friends here as Admiral Alexei said.

Alexei: Welcome to GDI, I am Admiral Alexei Bazarov. And who are you?

Leila: I am Leila Malcal, I'm the commander of W-O. These here are Akito Hyuga, Ryo Sayama, Ayano Kosaka, Yukiya Naruse, and Ashley Ashra.

Alexei: A very young soldiers, I see...

Ashley: Alright, get down the business. Who are you people and what business doing here anyway?

Ayano: Ashley! Don't be rude. We could've kick out if you say something like that!

Ashley: We have been confined in the cell after what happened the headquarter being taken over and go all the way here just to get arrested.

Alexei: Wait a minute. What's going on about your headquarter?

Leila: I'll be explain. We were about go on diplomatic mission to visit you to become our ally when we receive report that you've liberate some of the regions.

Akito: Then, we were attacked by unknown forces, probably the terrorist. But they are way advanced and quickly take out the security system and kill everyone. We were lucky to escaped in time.

Sayama: Not when you were damaged after battling an enemy knightmare.

Alexei: An advanced terrorist? Do you know where they from?

Leila: They don't belong to Holy Britannian Empire or Euro-Britannia special division. But they possibly be an individual terrorist.

Ashley: Not to mention those guys at the knightmare hangar bay. For what I saw, they're four-legged spider cyborg shoots lasers from their arms.

Alexei (thoughts): Wait a minute, cyborgs? Four-legged spiders? What do feel something so familiar?

Leila: Which is why we come here to help us. The EU won't know what's going on there and they're planning something terrible.

Alexei was quiet for a moment and he said.

Alexei: I wish I can help you. But I can't. Not without the president approval.

Leila: Then I like to talk to him.

Alexei: He's very busy on lot of politics so he has no time to call you.

Ashley: Well this is a waste of time coming all the way.

Leila won't give up so easily so she slam on both hands on the desk at him.

Leila: In that case, I would like to visit him. As a representative of EU, I am going to see your leader right now.

She said in serious tone. Akito and the others are surprised of how serious she is. Alexei look at her expression that she isn't a type of woman he don't want to mess with. So he said.

Alexei: You want to see him, yes?

She nodded.

Alexei: Very well, I have a transport to send you and your comrades to Colonial Global State of Earth. I'll tell him to know you're coming.

Sayama: Colonial Global State of Earth?

Leila: Thank you, admiral. And I would like my people to work with your people while we're gone.

Alexei: I'll allow it. My men will escort you there.

Leila and the others leaves the room to headed to the transport. Alexei leaned back on the chair to feel something familiar about the cyborg.

Alexei: Cyborg. Shoots laser from the arm. Could it be...

...

Scrin King MkII hangar bay

Elder and Inanis are walking in the hangar bay to show him around of five drone ships that are used in 3rd tiberium war. Inanis said to him.

Inanis (Scrin language): We only have few of drone ships to be deployed around the world but I fear that the humans living this world will work together and wipe us out then they'll use our weapons and technology for their own benefits.

Elder (Scrin language): Which is why we must be ready to start a full invasion when we make a right move to strike.

Inanis (Scrin language): I don't understand... Why are you helping me to accomplish your goal? You humans from your world beat the great army of Scrin and resist everything we tried to take over.

Elder (Scrin language): They're the ones who beat them, not mine and my group. We have hiding in the shadow watching them fighting among each other in bloodshed war. I, of course, going to create a large destruction across the world, starting with here.

Inanis (Scrin language): And what do you have me for?

Elder (Scrin language): To build a Scrin tower.

Inanis (Scrin language): The Threshold.

Elder (Scrin language): Exactly. Build a tower and your brethren will come and take this world in full force. As for me, I do join as well for full destruction on my image. The GDI, The Black Knights, Britannia, and all over country will be annihilated if we work together. So...

He give him a hand for a handshake.

Elder (Scrin language): Do we have a deal?

Inanis look at his hand for hesitation but he accept it as he grab his hand and they both shaking their hands.

Inanis (Scrin language): The Reaper-17 has follow your command, Grandmaster. And I shall follow too.

Under the mask, Elder was smiling for able to convincing the commander of Reaper-17 has join his side for the cause.

...

Ohgi was doing his hard work of reports to fixing the economy after the battle of Japan when a military personnel come through the door.

JDA personnel: Prine Minister!

Ohgi: What is it so important?

JDF personnel: The Great Kamon bridge in Kyushu block has been destroyed.

Ohgi: What!

JDA personnel: The enemy has cut off vehicle access at four other points, and the large numbers of assault landing craft are moving into the Genkai Sea!

Villetta came in the room as she said fo him.

Villetta: Ohgi! They beaten Fukuoka base and occupy Kyushu!

Ohgi: No way! Is it the Chinese Federation? They are the only one can closer between them and us. Have they declare war on USJ?

JDA personnel: No, sir! We identify that the crafts are bearing the flag of Japan!

Ohgi was shocked of Chinese Federation landing crafts are bearing on the flag of Japan and attacking the base at Kyushu.

Ohgi: This doesn't make a sense. Call the emergency meeting! Don't let them landed on every coast!

JDA personnel: Yes sir!

A personnel leave the room. Villetta goes to him and said.

Villetta: I don't get it. Who is leading those Japanese faction supported by Chinese Federation?

Ohgi: I don't know. But we have to be ready if something bad happen to this country.

...

The Chinese Federation landing craft bearing the flag of Japan has landing on the coast and took control the base, killing every JDF standing in their way. A shuttle came down the helipad as the door opens to see a former Japanese politician named Atsushi Sawazaki and a general named Chao leading this attack. They get out a shuttle and Chao said to him.

Chao: The area is secured. We'll proceed the operation.

Sawazaki: Good. It's time to take back what is mine and gain back the sakuradite as my own.

Chao: I hope what you're doing. The Japanese will see you as warlord and they will retaliate.

Sawazaki: Don't doubt my strategy, general! I promise you once we overthrow the puppet leader, I will have full power to construct a lot of army to large enough to destroy Britannnia since its crippled and invulnerable. And I give you a deal that I give every sakuradite to your nation to boost up the army and economy to avoid industry crisis. Now, set up the defenses. No ones goes in and out of this territory.

Chao: Understood, sir.

Sawazaki: Soon, I will show them how true liberation of Japan was. I bring back the Japan that was once before Britannia invade it. Japan will be mine-- no-- I shall create an Empire of Japan to become a superior nation.

He make an evil laugh so hard.