A lot of characters are given more prominent roles in this fan fiction series.
- When the writer began the story (prior to Episode 29 of Journeys which is Chloe's second focus episode), Chloe Cerise only had Journeys Episode 11 focused on her or gave her a significant role in the narrative. Blossoming Trail and Voyage of Wisteria is all about her struggles and growth, while everyone else in the Pokémon World only appears in the B-plot, which itself is focused on them realizing they've failed to be there for her and trying to figure out how to make up for that when she eventually returns.
- Out of Book 1's protagonists, Atticus had the least amount of importance to the plot with "The Ball Pit Car" being his only focus (and even then he turned into a Ghom and was out for the final two episodes). He gains his own arc in the story as he tries to deal with the idea that King Aloysius and the Unfinished Car may have been destroyed by the Apex.
- Amelia Hughe's appeared at the halfway point of Book 3 to give exposition of what she's been doing since the end of Book 1, helping to shed light on what the Train's purpose to Grace and Simon before she left to continue her duty to remove corrupted code on the Train and couldn't care less about this cult doing things in her "name". Here, she's more on helping to stop the Apex since she indirectly created it and has to stop Grace and Simon from learning who Hazel truly is and becomes the leader of the Quarto when Voyage of Wisteria starts.
- Hazel was mostly there to serve as a litmus test for Grace and Simon's empathy in the canon show. ''Voyage of Wisteria has her exploring the train with her mother as part of the Red Lotus Quarto and later has her own subplot to protect Warbler upon learning the music note denizen is a reincarnated Grace.
- One-One's a key player in the entire series but never makes an appearance in Book 3 (which is when the Blossoming Trail takes place). He's fully aware of the Apex this time around and is trying to stop them from doing any more harm.
- The Apex only appeared in four episodes in total (The Lucky Cat Car, The Mall Car, The Musical Car and the New Apex) and had no significance in Book 3 until the finale. Here, Blossoming Trail focuses on their dynamics and how much Grace's teachings have made them despicable. In Voyage of Wisteria it focuses on how they must live with the aftermath of their actions after the Fog Car shattered their innocence.
- Todd and Lucy are the most focused members of the Apex in both Blossoming Trail and Voyage of Wisteria.
- Bede has only two scenes in Blossoming Trail, but becomes the focal character of his own story Infinity Train: Court of Cyclamen, set between Blossoming Trail Acts 2 and 3.
- We see Bea's Pangoro in person instead of just in a photo due to the battle being three on three.
- Tokio Chisou was a one-episode character who was the reason why Goh decided to reject friendshipnote He would later return to the anime in Episode 102. He appears in all three stories of the trilogy, being the one who explains how he was on the Train in Blossoming Trail, exploring his adventures on said train in Knight of the Orange Lily and returning for Voyage of Wisteria once his memories return.
- Mr. Mime/Mimey was a background character in the anime, a big part of Ash's plans in this story.
- The canon show mostly focus on Goh and Ash's adventures, with the Cerise family in the background. In here, they're at the foreground.
- Professor Cerise role in the anime is basically to command Ash and Goh to go witness Pokémon phenomena with his interactions with his daughter limited due to that. Here, the story focuses on how his (in this story) neglectfulness in regards to Chloe heavily impacted his daughter and how little he knows of her.
- Parker Cerise has even less screen time than his sister in the anime, but in this fanfic, he has a storyline when he's trying to become more mature and be Yamper's trainer in his sister's place and also revealing that he knew more about Chloe's Hidden Depths than anyone else did.
- Yamper never had a big role outside Episode 11 and Episode 29 of Journeys. But here he is able to tell everyone in the Institute what Chloe really needed from them, he now partakes in more battles by his side, evolves and becomes a permanent member of her party instead of being relegated to the Institute.
- Kurene and Ikuo Fujihachi's major focus was in Episode 15 (which reveals Goh being a shut-in) but this reveals that they have done little to nothing to get their son anything resembling a social life.
- Akemi Tsutsuji a background character — albeit one who causes the entire story to happen — who gains her own spin-off story detailing her quest to find Chloe.
- Yeardley Lobelia was a Spear Carrier in Episode 11 of Journeys to be a contrast to Chloe. Here he has more characterization and was one of the catalysts of Chloe getting on the Infinity Train by goading her into fighting Ash and his signature "work in progress" line has a harsher meaning behind it, not to mention to be the recipient of the author's ire on Double Standard.
- Class 5-E had one significant scene in Episode 11 to talk over Chloe and question how she must be into Pokémon. Here they're all a bunch of bullies that drove Chloe to withdraw into herself and feel so worthless.
- Miss Jenny April only had a few seconds of screen time in the anime by the time the story was written yet she plays a significant role as to why Chloe didn't trust adults.
