The Darke Cats at the end of Darke are the first Warrior Cats.A huge group of cats moving into the neighbouring forest has a bit of a Dawn of the Clans vibe.
Beetle will become the Chief Hermetic ScribeHotep-Ra, the first Extraordinary Wizard, was best friends with Tertius Fume, the first ever Chief Hermetic Scribe. Septimus's best friend is Beetle, even if he was fired, and it's already been established he was extremely devoted to the job. It's not too much of a stretch for this to happen at some point near the end of the series, or possible even before. May even happen when Septimus becomes the Extraordinary Wizard. It already happened in Darke.
The antagonist(s) of Fyre will be the Darke wizards who created the Two-Faced RingThe ring has been the thing that united most of the antagonists in the series. It would be cheap for the last book to have a one-off villain like Queen Etheldreda, but the Darke Wizards have been mentioned many times. Septimus also saw two wizards in the Darke Halls saying, "Our time has come". They will take advantage of the chaos Merrin's actions have caused to escape from the Halls and use Darke Magyk to cause havoc. This is exactly what happens.