Lelouch dons a straitjacket in the Velvet Room, the same one that prisoners of Britannia wear in the series, rather than the old-school Institutional Apparel from the game.
Kallen's Persona resembles her Guren somewhat. Her evolved Persona takes it even further and it's very similar to her Guren S.E.I.T.E.N. from R2.
Milly's Thief Suit is based on the Cat Girl costume she wore for the welcome party for Arthur the cat in the anime.
There's an Accidental Pervert moment in Chapter 11 between Lelouch and Kallen that manages to combine their Shower of Awkward scene in Stage 3 and their Suggestive Collision from Turn 9. While taking a shower to wash off the champagne, Kallen uses their momentary privacy to have a conversation with Lelouch at the other side of the curtain, questioning Milly's motivations to be in the Black Knights. Annoyed by her persistent distrust, Lelouch snarks back and easily manages to anger the Fiery Redhead. She pushes the curtain aside and lunges for her switchblade hidden in her pink pouch like in canon, only to end up slipping on the wet shower floor and tumbling into a nasty fall. Lelouch reacts in time to catch her, but fails to keep his balance and only manages to cushion her fall, which leaves them in a compromising position similar to the one in R2 (plus nudity).
The Black Knights find designs of swimsuits and lingerie on top of Clovis' desk in his Palace's version of his office. This is a reference to the Picture DramaStage 8.75 where Princesses Cornelia and Euphemia inaugurate Clovisland — a themed water park designed by Clovis before his canonical death — while dressing in a couple of lingerie-inspired swimsuits also designed by him.
Zero and Bishop play chess in private in Ashford Academy's in-campus chapel, the same one where the canonical final confrontation with Mao took place in Stage 16. The chapel, or rather Shirley's Cognition of it, is the stage of the final battle of her Palace. And yes, Mao also bites it right after leaving the place.
Lelouch has a nightmare where Sayoko arranges 108 dates for him, which ended up happening in one episode of Code Geass while Sayoko was disguised as Lelouch. Up to Eleven here because in the nightmare those are just the number of dates for the first day of three weeks.
Remember when Kallen had to dress as a Playboy Bunny to infiltrate Babel Tower at the beginning of R2? Well, here she has to do it again for exactly the same reason in the Palace based on it, alongside all the girls in the Black Knights including Euphemia.
Eilonwy, Euphemia's Persona, is weak to Psi. This, per Word of God, is a reference to the Special Administrative Zone Massacre, where she was Geassed into killing the Japanese who had come there and another to Eilonwy herself who was mind-controlled in the third book of the novel series.
Euphemia/Noire carrying a large gun feels incredibly wrong for Lelouch. Likely a reference to the infamous "Euphinator" scene from Stage22.
The Cognitions of people in Shirley Fenette's wear the same white masks from a nightmare she has in R2 after Jeremiah uses his Geass Canceller on her.
Zero considers for a moment destroying Shirley's Treasure — namely her memories of him. This would have had roughly the same effect that using his Geass to make her forget him had in canon. He also considers using fire to do it, which is how he destroyed her diary in the anime.
Shirley is pressed by her own Shadow to kill Lelouch in a similar way to how Mao tried to do the same in Stage 14. And just like her canonical self was capable of shooting Villetta in order to protect Lelouch, Shirley stabbed her own Shadow in a sudden display of violence that none of her friends ever expected of her.
Once again Zero and his Black Knights crash a wedding like in Turn 09, albeit only a pretend one in the Metaverse between Cognitive people.
In Chapter 39, Kallen tells Lelouch during a discussion of the Love Triangle they find themselves in how she would follow him despite anything he did so long as he loved her; this is a reference to a Delivery Not Desiredletter◊ she wrote (video translation) that was included in the Complete Best CD soundtrack collection of the series, how if he had responded to her confession, Kallen would have followed Lelouch into hell during Zero Requiem.
In Chapter 40, Nunnally asks her brother to read her about Elizabeth the 3rd, the Last Queen of the British Islands and a favorite historical figure of hers. This is a Posthumous Character canonical to Code Geass' Alternate History without a real-world equivalent, who was first introduced during a history class in Stage 12. The bit about Nunnally being a fan of hers comes from a DVD Bonus Content skit from Season One titled "Britannia History Lessons". Elizabeth III seems to be the basis of Nunnally's Persona.
Leila's butler looked worried when she said she would take care of her and her guest's food herself. The narration doesn't mention the reason, but Leila is hilariously incompetent in the kitchen as seen in the third Code Geass: Akito the Exiled movie.
Chapter 41 has Nunnally comment that the only thing she needs to be happy is having Lelouch by her side and not change the world despite her secondary desire for the world to be a kinder, gentler place. This is the exact same thing she said after Zero Requiem.
In Chapter 41, Mao once again pulls off a No One Could Survive That!. This time thanks to his Persona possessing the Endure passive skill, an implant that automatically released epinephrine into his bloodstream originally intended to help him survive the experiments he suffered in Code-R, Shirley's Palace collapsing and dropping him into the real world, and literally insane determination to kill Lelouch.
In Turn 13, Shirley tells Suzaku that "nothing is unforgivable" and that "he only doesn't want to forgive him" in reference to Lelouch. Here, she says the same to Lelouch about his father Charles.
Kaguya references her "three court ladies" line from Turn 07 — in turn a reference to the celebration of Hinamatsuri, and more specifically to the dolls standing for the three court ladies serving the sake at the imperial wedding — when trying to convince Lelouch she's A-OK with him hypothetically two-timing on her if they get together.
The Student Council's summer trip comes about because Lloyd invites his fiancée Milly and her friends to Kamine Island while he investigates the ruins at Prince Schneizel's request. This exact development takes place in chapters 14 and 15 of the manga adaptation of Code Geass.
Milly says Lelouch would make a fortune as a male model. She makes a very similar remark in the second issue of the novelization.
Chapter 48 has Tsu drop the "do you know why snow is white" line.
The Camping Episode features the same waterfall and natural pool that appears in Stage 19. In a curious reversal from canon, it serves as the location for a tender moment between Lelouch and Euphemia rather than as the stage of a fight between Suzaku and Kallen.
The video from Chapter 49 is similar to the canonical Black Knights' proclamation on live television in Stage 8, down to them wearing their uniforms, face-concealing headwear, making sure the lighting will help to further conceal identifying features, and with Zero giving his speech to the camera.
In Chapter 50, the Black Knights enter Gao Hai's Palace resorting to a similar method Kallen, C.C., and Lelouch used in Turn 9.34 to infiltrate a Chinese Federation Army garrison. That is, by having everyone sans Arthur dressed in tantalizing dancing outfits and offering the soldiers a performance. Again, Lelouchcaught as much as attention as the girls, if not more.
Speaking of their dancing outfits, Kallen and Shirley's were "stylistically similar and distinctly Japanese with risqué twists". Going by this and other details, it seems they wore the same stage outfits their figurines had◊ in Code Geass: CODE BLACK 1st Live Encore from Banpresto's Ichiban Kuji merchandise lottery.
The Black Knights once again are trying to get in the way of the alliance between Britannia and the Chinese Federation by preventing the political marriage between Crown Prince Odysseus eu Britannia and Chinese Empress Tianzi.
Lelouch and Shirley go out shopping together to a mall in Chapter 54 under the excuse of buying a present just like that canonical selves did in Turn 03. Although, unlike the anime this is actually their first date as boyfriend and girlfriend and not a cover for something else, and the present is actually from him to her.
The Black Mask has the codename of Nebiros. In the Compilation movies, this was the Codename of Rolo, all but confirming that he is the true identity of the Black Mask.
Milly and Lloyd have exactly the same clothes they wore in the royal wedding reception in Turn 09. Milly in an Absolute Cleavage blue cocktail dress and Lloyd dressed in a "brown suit with gold epaulettes and a white undershirt".
Kaguya has her fancy pink kimono from the same episode.
During the Masquerade Ball, Lelouch commented that "under different circumstances, [he] might gave welcomed the opportunity to test his mettle against [Schneizel at chess] while incognito", which is exactly what he did as Zero at the royal wedding reception in Turn 09.
Lelouch signs the Masquerade Ball's guest book with the same alias he used in Stage 2 — Alan Spacer — to deceive Villetta.
When Gino Weinberg is introduced in Chapter 56, Lelouch recounts a bit of the history of his ancestors as seen in the manga Code Geass: Renya of the Dark.
Lelouch has a series of nightmares in the aftermath of the consulate party, two of them alluding tragic events from canon:
One has Euphemia suffering a psychotic breakdown, going on a machine gun rampage, mirroring the "Euphinator" incident from Stage 22.
The other shows Shirley laying on a pool of her own blood, bleeding out from a gunshot wound in her stomach as in Turn 13.
Suzaku Kururugi's Persona takes after his Knightmare Frame in canon, the Lancelot, and power wise it's equal to Kallen's Guren Jigoku Persona much as the two were always roughly equal enemies throughout the show.
Suzaku Kururugi's rapid ascent through the ranks resembles the one in canon, but the "career" path itself and the reason that makes him valuable to Britannia's interests motivating this are different. Namely, the fact he's a powerful Persona-user rather than an Ace Pilot, and his sponsor is Prince Schneizel himself instead of Lloyd and later Euphemia.
In Chapter 58, Leila has the same sleepwear — a "sheer pink nightgown, held in place by a pair of straps slung over her shoulders" — that she had in the second Code Geass: Akito the Exiled movie.
In Chapter 59, Kallen's Persona — based on her Guren from canon — is captured by Cognitive Xingke piloting the Cognitive version of the Shen Lu, specifically by getting snared in the cables of its Slash Harkens, just like in Turn 10. Unlike canon, the Black Knights manage to release her and she soon rejoins the battle.
Marrybell/West's Thief Suit seems to be based on her outfit◊ during Emperor Lelouch's reign in canon. Likewise, Oldrin/Oz's Thief Suit is based on her late-series outfit◊ as well.
Suzaku/Knight and Marrybell/West's Personas are named the same as their Knightmare Frames in canon — the Lancelot and the Elphaba, respectively. More specifically, their Personas are based on what inspired their KMFs' names — Lancelot du Lac from Arthurian Legend, and Wicked Witch of the West as named in Wicked.
Bishop's riding outfit is a reference to the pilotsuits◊ worn by her KMF squad in canon, both sharing the same color scheme — dark blue with red trimming — and other features like high boots secured by three parallel sets of belts.
Related to the above, there's an amusing bit of Double Standard in Chapter 62 when Lelouch accepts a ride from Bishop in her Cool Bike if you happen to remember Stage 0.916 "The Black King". The Audio Play recounts how Lelouch and Rivalz first met, involving the former saving the latter from losing a lot of money over a chess match, and ending with a very thankful Rivalz offering Lelouch a ride to school on the pillion seat of his bike. Lelouch immediately refuses with a "No thanks, I've never liked the idea of hanging on some guy's back", which is what makes Rivalz decide to upgrade his motorcycle to the Cool Sidecar he had his eye on as seen at the beginning of the anime. Evidently, Lelouch has no such issues if the rider is a Biker Babe instead.
In Ch 65, Kallen joins the Glinda Knights to aide in their assault on the Britannia cult's secret base in China, under the guise of being one of Marrybell's Royal Guards named "Karen Stratmann." This is not only a reference to the character's English voice actress Karen Strassmann but also something of a pun to the fact that "Kallen" and "Karen" sounds the name in Japanese.
During a conversation between Lelouch and Kallen, Lelouch toys with the idea of making her his Knight of Zero, a knight to outrank all of the other Britannian knights, if he ever somehow took the throne. He did exactly this upon taking the throne in canon, except making Suzaku his Knight of Zero.
Chapter 69 addresses the common fanon theory that Milly had a crush on Lelouch in the anime but never acted on it, and the Fridge Logic of the Ashford family not pushing for an Arranged Marriage between them despite him being still technically royalty and her mother's blatant intentions to push Milly to marry into nobility through a Marriage of Convenience with Lloyd. Specifically, the fic points out that Lelouch's hatred for his family makes him highly likely to vanish without a trace with Nunnally in tow rather than come back to the Imperial Family, something the Ashfords must have noticed and accepted, thus making them give up on the idea of an Arranged Marriage between him and Milly. As for Milly's alleged crush on Lelouch, the fic posits that's totally the case and that there were a number of reasons for her not acting on it. First, because she knew Lelouch was bound to mistake her for a Gold Digger agent of her family's aspirations and disappear. Secondly, because it soon became obvious that Shirley had it bad for him. And last but not least because he never gave her any indication that he liked her that way despite her frequently acting like The Tease with him, and Milly didn't dare to lose her best guy friend and confidant by confessing.
Parts of Clovis' Palace are based off of Shido's from Persona 5 — amongst others, his Palace has statues that gradually turn the female members of the Black Knights into more statues, a reference to how Shido had statues in his Palace that instantly turned the Phantom Thieves into mice. As for why the process is not instantaneous this time around? Clovis is a lot weaker-willed than the final target.
The protagonist plays a strategy board game with a girl in the tranquility of a church as part of their Confidant. Just change Shōgi for chess, and reduce the size of the church to a chapel.
Lelouch later has a nightmare where Arthur demands that Lelouch goes to bed, a clear reference to Morgana doing this frequently to the Persona 5 protagonist.
Azazel fights like a Dual Boss where one enemy is immune to physical attacks, and the other to magic — similarly to the Empress and Emperor's full-moon Boss Fight in Persona 3.
Azazel has two Standard Status Effects-inducing special skills, one that targets the girls in the party, and another the guys, just like Shadow Kanji in Persona 4.
Chapter 28 is titled "Swear to My Bones", which is also the name of the track that plays in Persona 5 during a Confidant's Rank Max event. And sure enough, Chapter 28 is when Lelouch maxes up his Confidant Rank with his girlfriend Kallen, with including the franchise's traditional Sexy Discretion Shot and everything.
There's something of a meta-joke about Kallen/Queen's Love Confession scene. It's not uncommon for players of the later games in the Persona series to have their Player Character accidentally enter a romantic relationship if they aren't familiar with its Dating Sim mechanics, or if the Dialogue Tree options at the turning point are too ambiguous. The latter happens to Lelouch here who tries to reaffirm the platonic elements of their relationship after getting caught off-guard by her Love Confession while his brain sorts out what to do about the non-platonic ones. Problem is, the girl in question takes his non-rejection as acceptance, and the next thing he knows, she's already hugging and kissing him, and thus making him realize that turning her down now would be even more damaging to their relationship than a moment before. As the games would put it, "there's no turning back..."
The chapters titles where the first three Boss Battles against Palace Rulers take place are allusions to the Battle Theme Music that plays in the initial ones in Persona 5. To be precise, "Blooming Villetta", "Blooming Viceroy", and the eponymous "Blooming Villain".
The Ruler of the Fourth Palace is so fixated on him that Lelouch doesn't send himself on a covert "special action" because it was doomed to fail. This is exactly what happens in the game if the player sends Ann to try and knock Shadow Kamoshida's crown off his head because he simply won't stop ogling her even in battle.
The non-canonical Persona Mermaid of the Lovers Arcana has the same design, elemental affinities, and a similar skill set as the demon of the same name in Shin Megami Tensei IV: Apocalypse.
Medjed's Back Story is roughly the same as Strega: Mao is a Phlebotinum Rebel resulting from Code-R's experiments to produce a Persona User and ended up opposing the protagonists due to some twisted sense of dispensing justice.
Medjed also got a kick of dragging people to confront their Shadows, something that almost certainly will get them killed without external help from the protagonists. Just like the perpetrator of the serial murder case in Persona 4.
The resolution of the fourth Palace is an even straighter Genre Throwback to Persona 4 than Futaba's Palace was where the team had to fight the Shadow to help its progenitor accept the ugly parts of their personality and ultimately awakening to their Persona.
There are numerous other parallels between the canonical ruler of the fourth Palace and the one in this story: Both Futaba and Shirley are the only daughter of a Cognitive Psience researcher who got killed by the Black Mask. They developed suicidal tendencies from their distorted desires. The Dungeon Crawling in their Palaces was heavy on exposition compared to previous ones. They both confronted a monster born from the depths of their own psyches who wanted them dead but triumphed over them with the Black Knights' help on top of making an important personal breakthrough. They ended up entering their own Palaces and awakening to their Personas in there, which they immediately used to help the party, but the effort took a lot from them and they ended up in a coma-like stupor lasting several days. Oh, and the two of them are long-haired redheads with ages in the high school range.
Shirley's Thief Suit is based on that of Kasumi Yoshizawa in Persona 5the Royal because of their shared characteristics. They're both red-haired athletes with strong if complicated feelings of admiration for the leader of the group of rebels changing criminals' hearts, making their Thief Suits take inspiration from his outfit and others cues from the form-fitting clothes they wear for their respective sports.
Mao survives the collapse of Shirley's Palace in a way very similar to how Ryuji survives Shido's.
Lelouch and Nunnally/Nemo defeat Mao/Medjed with a coordinated attack, just like the Co-Op Attacks Persona 3Portable.
Zorro — Morgana's initial Persona — is also briefly considered as a Code Name.
The Irregular's command structure (an older member serves as the strategist and general commander while a Wild Card takes point in the field) greatly resembles that of S.E.E.S. after the protagonist joins.
At one point, Arthur gets ferried around in a partially unzipped bag just like Morgana in Persona 5. The twist is that it's Nunnally's bag rather than Lelouch's.
Chapter 46 reveals that Lelouch has been spending a considerable amount of money and effort to keep Arsene, his initial Persona, relevant in battle — to the point his Warden calls it a "vanity project". He argues back that because Arsene is such a low-leveled Persona upon fusion, it's got more room to grow. In Persona 5 metagame, Arsene is indeed a favorite target for Min-Maxing projects because it's the only level 1 Persona of the game, and naturally, thanks to his cool design too.
Milly considers booking an overnight stay in the Amagi Inn in order to give the Student Council the "complete ryokan experience" during their summer trip, but the "sleepy town of Inaba" is located at the opposite side of Mt Fuji and thus it was too big of a detour given their planned destination. Furthermore, Milly also mentions Okina city, which is unlockable in the Updated Re-release of the game, and the geographic references match that of Fuefuki city in Yamanashi Prefecture, which was the real-life inspiration for Inaba.
Following the tradition that started with Persona 3, only one of the girls in the team is not a Lethal Chef. For added Hidden Depths, it's Milly.
Unlike Makoto Niijima in Persona 5, Leila Breisgau doesn't break the Lethal Chef streak present in the Social Links of the High Priestess Arcana from previous games.
During Chapter 48, Lelouch has a dream that subtly references the events of Persona Q2: New Cinema Labyrinth. Kallen has a similar dream which involves her fighting alongside Naoto, implying he is a member of the Black Knights in an alternate timeline the way the Female Protagonist is the leader of S.E.E.S. in an alternate world.
In a bit of a Take That! to the original Phantom Thieves of Hearts, Lelouch notices all the stridently voices on the internet calling for the Black Knights to perform a higher-profile Change of Heart than the ones before... and he completely ignores them. Lelouch has no issue raising the stakes because targeting influential corrupt people is what they do, and because he needs the public awareness of them in order to gain further access into Mementos, but no one outside the Black Knights and trusted collaborators gets a say on how they operate.
Dame's Persona has a skill set very similar to Haru's, including Gun skills and an arrangement of support skills, but replacing Milady's Psy-type attacks with Bless-type ones.
Just like in Persona 5, one of the consequences of failing to clear the fifth Palace in time is an Arranged Marriage, only not one involving a party member.
In Chapter 51, Leila gives Lelouch a tour of her Big Fancy House and shows him her father's car collection, including a Citroën H Van, and she comments that she toyed with the idea of bringing it into Mementos as a form of transport. In canon Persona 5, Morgana transforms into a van based on that particular model to transport the Phantom Thieves through Mementos.
Continuing from the above, in Lelouch's dream before it becomes an Erotic Dream thanks to Lilim, the oneiric version of Arthur does the same Voluntary Shapeshifting trick to replace their Burais that disappeared without reason. Furthermore, "Queen" ends up behind the wheel just like in the game.
Leila owns a CoolBike◊ and likes to ride on it for stress relief despite being inappropriate for a girl of her social standing, just like Mitsuru Kirijo in Persona 3. She even considered using it during the team's supernatural adventures too, but Lelouch found a better solution for their transportation problems first.
Like canon Futaba Sakura, Nina calls in her own change of heart.
In Chapter 53 it's mentioned that one of the candidates for Lucretia's Code Name was "Oracle", which was Futaba's callsign in Persona 5.
There are several Shadows/Demons from previous games in the Persona and Shin Megami Tensei series in the Fifth Palace to match its Chinese Mythology theme. For example, Zhen, Senri, Neko Shogunnote while he does appear in Persona 5, he's not a random encounter, Feng Huangnote same thing as with Neko Shogun; Feng Huang is (incorrectly) localized in English as "Phoenix", and Tao tie.
In Chapter 54, the Irregulars have a moment of Cuteness Proximity about Arthur, but Dalque/Power "proved to be too enthusiastic" and he complained that her petting was more like "button mashing" just like it can happen to Morgana in that infamous Funny Moment on 5/16 of the in-game calendar.
Lucia — Lucretia/Land's Persona — shares the same name and design as its namesake from Persona 3.
Lelouch intentionally made his costume and mask for the Masquerade Ball look like his Persona Arsene.
Chapter 59 is titled "The Bosses of Greed and Fear", taken from an excerpt from a line in "Rivers in the Desert", the boss theme against late-game antagonists and optional super bosses in Persona 5. The author also sneaks a few other lines of lyrics from the game's soundtrack into the chapter itself.
The fight against Shadow Gao Hai is basically a mix between Okumura and Shido's boss fights from Persona 5. Like Okumura, Shadow Gao Hai's transformation for the Boss Fight is underwhelming and doesn't become any stronger himself, instead relying on waves of mooks to fight the thieves, and he's also a Time-Limit Boss with the arrival of Cognitive Schneizel on his Avalon representing Gao Hai's idea of "ascension" to a higher stratum of society. The later stages of the fight parallel the Beast of Human Sacrifice, Wings of Human Sacrifice, and Tomb of Human Sacrifice from Shido's boss battle.