WARNING: The following contains spoilers from Star Wars Adventures #9 -10, now available from IDW Publishing.
Jedi Master Mace Windu and Count Dooku were the faces of Star Wars’ Clone Wars on their respective sides of the conflict because both were second in command to very powerful masters. Because of their control of the Force and individual skill with a lightsaber, a duel between them would have been a battle for the ages. Unfortunately, Windu and Dooku never fought in the live-action films or in an animated series. However, they did just cross blades in Star Wars Adventures #10 -- by Michael Moreci, Michael Avon Oeming, Chris O’Halloran and Johanna Nattalie – marking the first time they have fought in canon.
Star Wars Adventures #9 saw Master Windu investigating a communications blackout on the planet of Ridlay. When he and his Lightning Squad arrived, they found that everything was abandoned. Eventually, one native appeared and warned them of the ghosts that were haunting the planet, so Windu went with the native to where the locals were hiding. At his request, they showed him the Ascension Well where the ghosts emerged from, only to find Count Dooku rising up from the hole.
Faced by a Sith Lord, Windu drew his amethyst blade and confronted his sworn enemy as Star Wars Adventures #10 began. Their duel was short but fierce, with flashes of purple and red lightsaber fire sparking as the two of them traded verbal barbs. Count Dooku insulted Windu’s lack of dueling imagination using his signature Dun Möch, while Windu tried to figure out how Dooku was involved in the angry ghosts caper.
It turned out that the ghosts were a species of gaseous beings that could solidify just enough to influence solid matter. The ghosts emerged from the Ascension Well every 50years when Ridlay was in total eclipse, and they were normally not an issue. This time, though, Dooku had influenced their hive-minds into attacking the locals and Windu’s troopers as part of a plot to make a Separatist army that literally couldn’t be touched. However, when Windu arrived, Dooku abandoned the plot and fled as he was wont to do.
Dooku and Windu had a history long before the Star Wars prequels began. Before Dooku was a Sith, he was an esteemed Jedi Council member. As Windu’s senior by 30 years, he saw Mace grow up and mature in the Jedi Order. That’s why he referred to Windu as an “old friend” in this comic. That’s also why Windu tried to confront Dooku directly in Attack of the Clones. If he had been able to fight and defeat the former Jedi on Geonosis, the Clone Wars would have been very different. But with Jango Fett there for protection, the playing field was not even. And even if he had been presented with a fair fight, a Master Windu victory wouldn’t be out of the question.
Dooku was one of the most esteemed duelists in Jedi and Sith history because of the combination of the Makashi style and his trademark, curved lightsaber hilt. That notwithstanding, Master Windu was also one of the best. If the two spared as Jedi, Dooku would probably win the match because he was the better all-around duelist. But if this issue's fight had continued with Windu as a Sith, Windu would have been able to turn the tables. The use of his Vapaad style would have given him an automatic advantage while fighting against any dark side user.
So, while Star Wars fans never saw a knock-down, drag-out fight between these two icons, it seems likely that Windu would've bested the former Jedi.