At the start of the story, Carly arrived at the Player's house and asked him to be her assistant to which he agreed.
In the first event of the story, the Player and Carly tried to ask Leo and Luna where Yusei was, and due to a misunderstanding, ended up Dueling them with a wager that if the Player and Carly won they would then tell them where Yusei was. After winning, Carly gave the Player two copies of two of her "Fortune Fairies".
In the second event, the Player and Carly asked her informant Rathie about whether rumors of Yusei being chased by Sector Security were true, to which he confirmed. As payment, she gave him a "The Unfriendly Amazon" figure. They arrived at Sector Security and snuck in only to be stopped by Hose. Trudge and Mina intervened and after some thinking, Trudge teamed up with Mina and Carly teamed up with the Player in a Tag Duel. After winning, Carly gave the player with two more copies of two more of her "Fortune Fairies".
In the third event, the Player and Carly headed to Yusei's hideout to find out more about him. Once inside, they found Rally Dawnson who tried to send them away. Yusei soon returned and Carly wished to interview him, but Rally intervened with a Tag Duel and a proposal: If Rally and Yusei won, Carly and the Player would leave him alone, but if Carly and the Player won, Carly could interview Yusei. After winning, Carly gave the Player her last two copies of two of her "Fortune Fairies".
In the final event, the Player and Carly found Jack so she could get her big break. The found him at the Stadium but as she was about to interview him, Mina stopped her. Carly decided to bait him and by doing so, Jack challenged Carly to a Duel with Mina as his partner and the Player as hers.
In the end, Jack kept his word and allowed Carly to interview him. However, Carly decided not to write the article since she only wanted to write articles that supported and encouraged people, a dream she had since she was a little girl, so she kept the secret that Jack was from Satellite safe. At her apartment, she told the Player that with him at her side, they could get even bigger scoops.
Upon completing the story, the Player received one additional copy of all the "Fortune Fairies" and the photo "Carly Carmine - No Looking Back!"
Dark Signer Carly's Story
To unlock Dark Signer Carly's story, the player must clear Jack's story, and then take Carly to see Lenny at the shoreline and select the option "Look at partner in a new light". Like other Dark Signer characters, Carly appeared between the evening and the end of the day.
In the first event, the Player and DS Carly found Crow and Leo. She reminisced about helping people to make a difference, but then she thought of the negatives, like how having too much to handle had caused her rebirth as a Dark Signer. Crow and Leo challenged them to a Tag Duel to which they accepted.
In the second event, the Player and DS Carly encountered Luna who planned to Duel her. Trudge stepped in and reminded her of how kind she used to be, but DS Carly told him that the other Carly was gone and taunted him. Trudge offered to be Luna's partner for a Tag Duel, and DS Carly had the Player as her partner.
In the third event, the Player and DS Carly went after Akiza. After dealing her story, Mina stepped in and tried to reach her but to no avail, and she challenged them to a Tag Duel.
In the final event, the Player and DS Carly confronted Jack. After trying to reason with her to no avail, Yusei stepped in and told him not to give up. DS Carly challenged Yusei and Jack to a Tag Duel with the Player as her partner.
In the end, she decided to let them live, however she declared the next time she met them she would destroy them and that she would start with Yusei.