After you defeat Rebecca, if you talk to Roland he says this.
Roland: That girl is no match for Master Seto, but in ten years she will be ready to take on the world.
When the Neo Ghouls take over the Egypt Exhibition, you have to battle your way through 5 opponents without being able to heal in between. Clearing this challenge makes Yugi and Joey declare that you are an awesome duelist.
Marik praying for his parents and those he hurt before you duel him.
Marik: Father, Mother... And all those people I harmed... I hope that the sun shines upon your spirits.
One scene in the ending has Roland wondering what to do with Seto and Mokuba away. He decides to perform another Kaibaman show to bring hope to the children of Domino.
The ending, as everyone waits for your safe return and goes to meet you there. Even ones like Weevil come (but he tries to deny his true reason of waiting for you).