Just as most other YGO fanfiction writers, I wanted to get right on writing about the show while it was airing, not waiting for the whole thing to wrap up to tell stories about the characters. My imagination was sparked almost immediately! Of course, since I came in during reruns for the first 26 episodes and was around for first-run of everything else, that meant almost everything I wrote ended up not quite fitting into canon when all was said and done. I brought in canon elements as they were introduced in the episodes, and sometimes that meant my stories contradicted each other (slightly), but that was alright with me. I remember calling Marik and Ishizu by their Japanese names the first time they were mentioned in a story, but when it was time for them to take center stage several stories later, their dub names were known and I preferred them, so I used those.
I brought in popular fanon tropes of Yami Yugi and Yami Bakura being able to form bodies for themselves. Judging from Ballistic in Boston, those bodies could be destroyed but their spirits would endure and could make another one. The bodies weren't mortal, strictly speaking, but they were solid. I suppose it was similar in some ways to the bodies the sentient Gem characters can create on the cartoon Steven Universe.
I also wanted to have the characters go on fun mysteries. Everyone and their dog thought I was using Scooby-Doo as inspiration, but it was actually Nancy Drew and The Hardy Boys (which may be where Scooby-Doo writers got their inspiration, actually). The mysteries were chock-full of intrigue, dangerous situations, and cliffhangers, just like my inspiration. That was great for me, since I have always been a hurt/comfort writer. Characters could get locked in safes, lost in the snow, end up mind-controlled, or other, weirder things (like one time when Duke gets hanged). Logic and reality played very little part! Characters would be up and at 'em again within days or hours, again like my inspiration. I knew it wasn't realistic, but realism held little attraction for me.
In addition to my multi-chapter mysteries, I wrote oneshot stories focusing on various characters. Usually the oneshots would focus on my favorites, but not always, if I got an idea for characters I didn't normally write for. The oneshots often had hurt/comfort situations too. Other times, they were slice-of-life friendship or sibling squee.
When canon finished, I still had ideas but I wasn't keen on writing in the old verse where so many things contradicted canon. I say that there are two main timelines, but really, there have been three. The second one happened around this point. While it brought in some elements from the first timeline, it tried to adhere closer to canon and took place post-canon, with the Yamis gone. These stories were mostly dark, such as Life After the Tears. I also started Dragons at Dawn a bit later and stalled on it sometime later, after sparse updates.
I had long felt betrayed about the revelation of Zorc as part of Yami Bakura, which was also part of the reason for the middle timeline. I still loved the character as I thought of him, solely the Thief King, and I didn't know what to do with him anymore. I don't remember how I finally got the ideas for having him pulled apart from the fusion with Zorc and survive, but it happened several years later. What became my current timeline started then, again mostly with darker stories but occasionally a lighter one. I didn't do a lot of advancing for this timeline after Burning Starfire stalled, but every now and then I did, and I'm working anew on this timeline now. I managed to move Dragons at Dawn to the current timeline, something I had planned to do with it shortly before I stalled.
Along the way, I have always experimented with mini-timelines consisting of two or so stories. Paper Flowers and Candy Clouds happened during the time of my first timeline, but they are a timeline unto themselves. Around the time I started tinkering with the beginnings of my current timeline, I also tried things such as my Alone Again, Naturally timeline, where the characters are a little older and Duke has wandered down a bad path because of feeling bitter and alone. And off and on through the years I tried things where characters paired off, such as Seto and Tea. Lead Me Through the Fire was also considered a timeline unto itself until I decided to incorporate it and its sequel Close Your Eyes, Clear Your Heart into my current verse, with a few minor tweaks to fit.