While there aren't many of these, there are a few examples.
- Interseason-crossovers, featuring alternate universes. That this one was Canon doesn't hurt.
- Likewise, interseason-crossovers, not featuring alternate universes.
- Stories where the Digidestined learn to Bio-Merge, while not common, do exist. Notably, Dimensions uses this.
- Fix Fics about the contested epilogue, usually replacing canon couple Matt and Sora with the Fan-Preferred Couple Tai and Sora.
- Rewrites of the entire second season are extremely common, usually done for the purpose of patching up all the plot holes. Most of them follow the Emperor arc fairly closely, but after that, all bets are off.
- It is extremely common, especially on Fanfiction.net, to find Slice of Life shipping fics, moreso than fics taking place in the canon universe, usually limited to the cast of the first two seasons.