In canon, Lelouch ordering the retreat from Narita was because the Guren had its Radiant Wave Surger damaged by Suzaku, which his whole battle plan depended on. As this essentially abandoned the Japan Liberation Front to be destroyed by Cornelia's forces, this strained the Black Knights' trust in him. Here, the retreat is due to the Decepticons showing up and completely turning the tide of the battle. The rest of the Black Knights obey mostly without hesitation because they are getting slaughtered by the Decepticons.
In the Prime episode Partners, Arcee letting Starscream escape was a case of Revenge Before Reason, as she wanted to kill him to avenge Cliffjumper and ended up underestimating him. Here, this point is not present, as Cliffjumper is still alive. Rather, his escape is a result of Starscream managing to appear pathetic enough that Arcee and Kallen let their guard down and let him get too close to them.
In the Prime episode Stronger, Faster, a Synthetic Energon-enhanced Ratchet really lets Optimus have it—blaming him for the Autobots "squandering their resources," what happened to Cliffjumper, and not being proactive enough against the Decepticons, triggering Arcee's Berserk Button. Due to Cliffjumper being alive in this story, he triggers Kallen and Lelouch's instead of when he brings up Naoto's death and insults Lelouch after he reflexively activates his Geass.
In Tohdoh the Miracle Worker, Lelouch ordered the Black Knights to retreat from battle after finding out Suzaku was the pilot of the Lancelot due to shock at having to fight his best friend. Since Lelouch pretty much knew this from the get-go in Code Prime, he instead calls the retreat because Britannia has sent a massive group of Knightmares to reinforce the prison.
The dialogue between Zero and Suzaku in Tropical Assault is modified to account for the fact that Britannia and the Decepticons are fighting side by side. Zero explicitly states that he knows Suzaku killed his father, Prime Minster Kururugi, and questions the latter on if he'd follow Britannia or the Decepticons if either gave him an order he could not complete in good conscience.
Kallen and Suzaku's conversation on Kamine Island was, in canon, a case of Both Sides Have a Point, with Suzaku noting that Zero's actions have resulted in many unneeded deaths, while Kallen rebukes him by asking what purpose her brother's death would have served. Here, due to the Black Knights undergoing Adaptational Heroism due to their alliance with the Autobots, while Britannia undergoes Adaptational Villainy from working with the Decepticons, the conversation is firmly a "The Reason You Suck" Speech toward Suzaku, who struggles to find a way to rebut her statements.
The SAZ Massacre. In canon, it was caused by Lelouch accidentally Geassing Euphemia, leading to her ordering the rest of the Britannian Army to slaughter the citizens. Here, it's caused intentionally by Megatron having her kidnapped and replaced with a Pretender, and while she doesn't give the order, the Britannians still attack the civilians under Emperor Charles's (or rather Soundwave's) orders. Not to mention that there are a group of people still alive and being tended to their wounds in the Ark.
In canon, Ashford Academy was seized by the Black Knights as a headquarters during the Black Rebellion so Lelouch could protect Nunnally while claiming to the Black Knights that it was of strategic importance. Due to Lelouch moving Nunnally to the Ark, which is the base for the Autobot/Black Knight alliance, Ashford is instead seized by the Insecticons, who take Milly, Rivalz, and Nina (along with Arthur) hostage under Megatron's orders.
Lelouch and Suzaku's "Is there anyone you could ever hate so much that you actually want to kill them?" discussion has its context changed on multiple levels.
In canon, Suzaku was talking about Zero, unaware that he was Lelouch. Here, he knows Lelouch is Zero and is talking about Megatron.
In canon, Suzaku said this while preparing to fight the Black Knights. Here, he has joined forces with them.
In canon, Lelouch told Suzaku to embrace his hatred. Here, he cautions Suzaku to keep his hatred under control, reminding him that many Britannians and Japanese alike viewed him as a hero.
Finally, in canon, Suzaku made the call on Euphemia's phone. Here, as she is still alive and has said phone, he uses his own phone instead.
Nina's Roaring Rampage of Revenge is different here. While the reason for it is for Euphemia like in canon, as opposed to Nina wishing to avenge Euphemia's death at Zero's hands, she wants to save Euphie from the Decepticons after learning of her abduction.
The Black Rebellion still ends in failure and defeat for the Autobots and Black Knights, but unlike the canonical failure which was caused by Zero abandoning the Black Knights to rescue Nunnally on Kamine Island, the cause of failure is brought about due to the Decepticons launching a full-scale assault on the Tokyo Settlement after destroying Pendragon. The Black Knights and Autobots, already exhausted from fighting the Britannian forces just moments ago, are forced to retreat to the Ark when they end up losing half their forces.
Furthermore, Zero still disappears from the battlefield, but this time due to being teleported away against his will.
Also, Jeremiah still has his "I'm begging you, please die." moment, but now it's directed at Wheeljack after he innocently questions if this is "that Orange guy" he'd been told about, as opposed to Zero deliberately pushing the Orange button.
Suzaku still says his "Your very existence is a mistake" line at the end of R1. Here though, instead of Lelouch/Zero, it's directed (very accurately, and rightfully so) at an unaffected Megatron.
Optimus's blade catch, "Megatron! Begone!" Pre-Asskicking One-Liner and subsequent beatdown of Megatron is present. But unlike the Orion Pax three-parter, where he does this after regaining his memories, here he does it after breaking free of Megatron's Dark Geass.
Code Prime - R2: Revolution
The Knights of the Round attempt to launch an assault against a new ruler of Britannia, but instead of it being Emperor Lelouch, it’s Megatron following his conquest of Pendragon.
Additionally, while Bismarck has the same last words here as he did in Code Geass canon, Marianne is actually present to hear said words.
Also, four Knights of the Round still partake in the assault like in canon, and three of them remain the same with Bismarck, Gino, and Dorothea. The fourth one is Anya/Marianne, as Monica, the fourth Knight from the canonical assault, defected to the Black Knights after the Black Rebellion.
Bismarck's death was still due to his Geass being overcome, but where in canon Suzaku moved faster than his Geass could track him, here it is due to his Geass outright being erased by Devastator's Geass Canceller.
Mt. Fuji is destroyed by Lelouch like in canon, but instead of being destroyed to cripple the Black Knights and Schneizel’s forces, it’s instead blown up at the insistence of Kyoto to cut off the Decepticons’ Energon supply, and serve as a symbol of resistance against Megatron.
When Lelouch destroys Mt. Fuji, he has his "hope begins now" line from canon, and promising a Heroic Sacrifice won't be in vain. In canon, it was for Urabe after he sacrificed himself to save Lelouch from Rolo. As Urabe is still alive, it's instead for Dreadwing, Cliffjumper, and the other Black Knights who lost their lives during the Black Rebellion.
In canon, when Megatron obtains the Spark Extractor and goes through the Space Bridge portal, Bumblebee snatches it from Megatron's grasps. Here, it's Suzaku.
In canon, a shield generator that was part of the Iacon relics was obtained by Knock Out, and later destroyed by Bulkhead. In the story, the Autobots and Black Knights manage to obtain it thanks to Jetstorm and Safeguard, and plan to integrate it into the Ark’s systems.
The High Eunuchs plan to join the Chinese Federation with another superpower by marrying their Empress to a powerful figure. In canon, it was Odysseus and the Britannian Empire. Here, Schneizel is the one Tianzi is expected to marry to join the Federation with the Decepticon Empire.
In canon, Jean was convinced by Ayano to pull a Heel–Face Turn and stop Shin from killing Akito. Here, it's Shirley that talks her down.
Due to Lelouch being in the EU during the fight in the Chinese Federation, Wizard is the one who records the High Eunuchs insulting their people and confessing to the death of the Empress' parents, then broadcasting it to incite riots all over the Chinese Federation.
Like in canon, Jeremiah pulls his Heel–Face Turn by swearing himself to one of Marianne's children. Instead of Lelouch like in canon, it's Nunnally.
The Relic that the Autobots and Black Knights recover in Chapter 22 is the Skyboom Shield. Unlike in Armada, where the shield was created from three Mini-Cons combining, the Skyboom Shield was forged by Solus Prime, and only a Prime can unleash its full power.
Due to Hardshell dying earlier than in canon, V.V. as Nemesis Prime is the one to shoot a retreating Bulkhead in the back at the end of the story’s version of “Toxicity”.
Megatron still gets to say his ‘You’ve hit rock bottom’ speech, but its towards V.V. after he finds him crawling towards the Thought Elevator rather than Starscream in an Energon mine.
An ally of Optimus chooses to sacrifice the future of Cybertron by using the last of the energy in the Forge of Solus Prime to bring him Back from the Dead. But while in canon this was done by Smokescreen because the latter didn't want the responsibilities associated with being Prime, here it's the entire science team plus Nunnally, who all want Optimus to live. Additionally, the issue of denying the Autobots a future is sidestepped by Megatron having Damocles pointed right at Horai Island - if Prime hadn't been rescued, there would not have had any Autobots to have a future.
In Transformers: Prime, an incensed Optimus ends his speech with the words "Megatron must be destroyed." after seeing Megatron nearly kill Raf and determining the Decepticons will never mend their ways, aiming to kill Megatron because of his attempt on the child's life. Here, before the battle of New Kaon, Suzaku ends his dialogue with that exact same line, only for the more noble goal of killing Megatron to stop his plans and save the world.
