This page will address those persistent rumors about this pairing, and tell you the facts straight up.
I hear Seto and Shizuka end up together later in the series. Is this true?
False. Shizuka was only an active character in the Battle City arc, and did not join the gang on their journey in the later arcs. Therefore, nothing could have happened between the two if she wasn't even there.
But doesn't Seto fall in love with Shizuka after she writes that song for him?
False. This was just a simple rumor that got spread like wildfire on the net in early 2003. It does sound like something Shizuka could do, but it never happened. And come on, this is Seto were talking about - he'd never go soft on a song!
So what exactly is the relationship between Seto and Shizuka?
Actually, I don't think you could properly call what they have a relationship ^^; The truth is, they barely ever interact. The only major interaction they've ever had was the infamous blimp scene. Other than that, they've just kept their respective distances.
What is this infamous blimp scene about anyway?
It is the scene that gave life to the Silentshipping fandom.
In episode 85, Yugi-tachi asks Seto to land the blimp, because Ryou got injured from his duel with Yami and needed medical attention. But Seto flatly refused to grant their request, since they were in the middle of the tournament. Shizuka then pleaded with Seto, saying that he should know that life is more important than any duel, and he ended up calling the medics on board to look over Ryou.
The important thing is that of all people, she was the only one who was able to get through to him. It was quite a short scene, but was enough to win over many fans ♥
OMG I found evidence of them in the manga!
Unfortunately, Takahashi-sensei has stated from the beginning that he wanted friendship to be the main theme of the series, so there is no official canon between any main characters. Maybe you were looking at a doujinshi and got it mixed up ^^;
I hear Shizuka is the reincarnation of Kisara (from the Egypt arc). So that means Seto and Shizuka are really meant to be!