- Kasumi Yoshizawa: An accomplished young gymnast who enrolls in Shujin Academy around the same time as the protagonist. She is a great admirer of the protagonist and one of the few people in school who treats him kindly. Though not an official Phantom Thief at first, she briefly assists the protagonist during the events of the original game. She wears a black mask with silver accents and wields rapiers and rifles in battle.
- Takuto Maruki: A part-time school counselor and researcher of cognitive psience who enters Shujin Academy following Kamoshida's arrest. He is a genuine, understanding person and always helps students whenever needed, being among one of the more popular members of the school faculty. He is one of the protagonist's new Confidants in the story.
- Jose: A mysterious young boy who researches humans and helps the Phantom Thieves in Mementos. Flowers and star stamps can be collected in Mementos, and the protagonist can trade these items with Jose in his shop: flowers are traded for items, and star stamps allow him to change Mementos' cognition, improving the rate at which rewards are given, such as experience, money and items. He can also turn Will Seeds into more powerful accessories with unique skills that greatly aid in battle.
Royal introduces a third semester that doesn't appear in the original Persona 5. In this mysteriously altered reality, the party's various wishes have been granted:
- Morgana is a young, attractive human boy.
- Ryuji's leg was never broken and the track team is restored, with Ryuji being its leader.
- Ann is now happily hanging out with Shiho, who was never sexually assaulted by Kamoshida, yet transferred schools for other reasons. Much to Ann's delight, Shiho is now a volleyball ace, and will be transferring back to Shujin.
- Yusuke's teacher, Ichiryusai Madarame, seems to display none of his prior distorted desires and goals, and the original "Sayuri" is exhibited in an art museum using Yusuke's mother's name.
- Makoto's father is alive, and she and her sister have a much tighter, sisterly bond, feeling like a complete family.
- Futaba's mother, Wakaba Isshiki, seems to have always been alive. She's entrusted Sojiro to take care of her daughter while she's working on her research, and the three are frequently seen together, acting as a family.
- Haru's father, Kunikazu Okumura, is also alive and no longer corrupt. Instead, he is now a kindhearted businessman with no interest in politics, and genuinely takes care of his daughter like he once did, almost to the point of overprotectiveness, teasing her about her relationship with the protagonist.
The protagonist realizes how strange this all is, and is approached by Akechi, who is also cognizant of these discrepancies. Akechi clearly remembers assassinating both Wakaba and Okumura, and confronting his cognitive self in Shido's Palace. Together, they investigate these strange events.
In order to unlock the third semester, the Councillor Arcana Confidant must reach rank 9 prior to November 17th. If it does, it will max out automatically during that day. Failure to max it out will result in the same end scenario as the original Persona 5.
- A new location added is Kichijoji: A popular spot in Tokyo that the protagonist can visit. With a mix of new and old, various cultures and personalities clash in this area that attracts men and women of all ages.
- A collaboration with DARTSLIVE: DARTSLIVE’s latest darts machine, DARTSLIVE3, is fully reproduced in-game. The protagonist can invite his fellow Phantom Thieves to play darts together. This is a completely new minigame in the series, and uses the PS4's motion controls. Playing will increase the ally's respective Baton Pass Rank to help in battle.
- The Phantom Thieves can play billiards, an activity which can increase a random Social Stat. In addition, it can help boost the group's Technical rank, increasing Technical damage and down rate.
- The protagonist can invite a teammate to Jazz Jin to drink virgin cocktails. Depending on the drink, certain stats of party members can be boosted, or they can learn new skills.
- The protagonist can visit an old temple to meditate, increasing his maximum SP.
- A clothing shop has been added where instead of being washed, Sooty Clothing can be traded in for points, which can be redeemed for rewards.
- Numerous other vendors have been added, in old areas as well as Kichijoji, selling more unusual or powerful items, usually accessories.
- The protagonist can invite his Confidants to an aquarium in Shinagawa, a new Confidant hangout.
- Another new hangout spot is Nakano, a shopping district filled with many trendy stores.
- Yoshizawa is one of the new Confidants the protagonist can hang out with. Her Arcana is the new, unnumbered Faith.
- Her Confidant abilities allow ambush from a distance with a grappling hook, and help the group avoid being surrounded by enemies when they're attacked.
- The protagonist can also bond with the aforementioned school counselor Takuto Maruki, of the new Councillor Arcana, numbered with the Arabic numeral 1 rather than the Roman numerals of the other Arcanas.
- His Confidant abilities grant the protagonist a chance to automatically remove status effects inflicted on him and automatically recover SP when it's low.
- Instead of being automatic, Goro Akechi's Confidant is now leveled up by hanging out with him.
- His Confidant ability is Sleuthing Instinct, which gives the protagonist a chance to instantly reveal a random affinity of an enemy at the start of battle. The upgraded version of this, Sleuthing Mastery, has a chance to reveal all affinities of a single enemy.
- Some original Confidants' abilities have been modified, being able to grant the protagonist new perks as well.
- The protagonist can bring Caroline and Justine touring around Tokyo, separate from their Confidant events, and they will reward him with Skill Cards for doing so.
- Similarly to female Confidants, the protagonist can now give gifts to male Confidants.
- The protagonist's free time has been slightly rearranged on the calendar.
- In addition, on certain evenings, the protagonist now gains additional, but more restricted free time, granting him the ability to perform activities within Café Leblanc.
- Most of the daily activities from the original game have been modified or expanded.
- A "Thief Assist" command has been implemented during the daily life sections of the game, with the intent of helping players navigate the options available to them on a daily basis.
- The Valentine's Day event is now updated with additional content.
- For the first time in the Persona series, White Day can be celebrated, which occurs prior the protagonist's departure from Tokyo. He can go on a date with any romantic partner. If he doesn't have one, he ends up hanging out with Sojiro.
- A new palace appears alongside an additional layer of Mementos as the available dungeons for the third semester.
- There is a new area in Mementos with a brighter, monochrome coloration, noticeably different from the previous areas seen in the original game. Enemies from the Depths of Mementos and the Qliphoth World can be encountered there. After exploring it once, fixed groups of much stronger variants of past enemies will sometimes appear. These enemy groups cannot be negotiated with.
- During the third semester, the party will receive new, stronger third-tier ultimate Personas, as a result of a fusion between their initial and second-tier Persona. In the process, each member will receive a special, signature skill.
- Akechi returns as a playable character in his Black Mask attire together with Loki.
- The Phantom Thieves have unison attacks called "Showtimes," unlocked over the course of the story, where two members can unite and attack an enemy together. It uses no resources, just like All-Out Attacks, and works even for enemies that cannot be Downed, though only one enemy can be targeted.
- New types of Shadows can appear in Palaces and Mementos:
- Savage Shadows are exceedingly strong enemies with a glowing red aura that cannot be negotiated with unless their health is reduced to very low levels (about one-quarter).
- Disaster Shadows appear, which have higher stats and will only attack when they are targeted first. They drop rare items and cause an explosion that damages nearby enemies once they are defeated.