Check out the histories of the Houses in the HoH series, for character and enemy ideas. You might even have your characters re-fight the schism wars, or take part in Pralix's epic campaign...
The Houses of Hermes Series give good overviews of Hermetic history, giving some good story hook ideas, if you're interested. There's also supplements on Rival Magics, Ancient Magics and such histories, including bits on the Order of Odin, and its formidible war against the OoH.
Books on the Dark Ages are incredibly common. Pick one or two up, or spend a day browsing Wikipedia.
Pay especial attention to HoH: Societas (Ex Miscellania) for good ideas for Hedge Wizards. The defining feature of the Dark Ages for the Order of Hermes was the prevalence and relevance of Hedge Wizards and the tensions leading up to and the outbreak of the Schism war.
Other Awesome events to play with potential alternate settings/endings are:
the Sundering of Tremere
the Corruption of Tytalus
the Betrayal of Verditus
the first Crusade
the Odin Wars
the Merinita Civil War (forget the official title)
the Siege of Cinterra (more recent event, ongoing -- just the invasion of the Danish islands, really, but Bjornaer are such drama queens...)
the Swearing of the Witches of Thessaly and Sihir of Iberia (over Flambeau objections)
The Donatores had the opening battles against the Cult of the Dead in Normandy, which also would make for a great story.
There have been a couple of discussions of good hedge-enemies on these fora. Some good ideas might be:
Craft Magus renegade with some way to disguise or shroud cast reliably, who launches a campaign against the nobility of....wherever.... by knocking down castles and arming the peasants.
Pharmacopean leaders of a pagan group who command hold-out clan of super-buffed warriors (a la Asterix and Obelix)
A Hedge Wizard-petty king who really, really doesn't want to give up his holdings upon swearing the Oath.
Note -- you can give the Hedge tradition multiple powers/person (i.e. Whistle up the Wind and Craft Magic, Shapeshifting and Entrancement, Nature Lore and Beast Summoning etc...) and can even give each tradition a handful of incantations they know outside their special power (left-overs from Mercurian rites or Druidic incantations, etc.)
With Parma, they can be quite powerful.
Just follow the universal rule of Ars Magica, and it will work for almost any pre-modern period: Be creative, and let the flavour soak in. The history is the backdrop; the story comes from your imagination, and the best hooks will be viable in any time frame.
The Supplements shouldn't be used as story crutches. The stories are ideas, not orders set in stone. The service they provide is in 1.) Providing a really rich and flavourful RPG system with good story seed ideas and 2.) Way, way more importantly, BALANCING that system mechanically, so that its enjoyable and challenging.
You don't need any supplements more than they've provided to make a really good dark-ages game.