I think I’ve figured out Mace Windu‘s secret rule during the Clone Wars. Played by Samuel L. Jackson, Mace Windu had a unique rank in the Jedi Order. He is the “Master of the Order,” a trusted Jedi Master elected to lead the High Council. The Master of the Order is the one who has the final say in any ᴅᴇᴀᴅlock, explaining why Mace was key to many decisions during the Clone Wars.

Steven Barnes’ novel Mace Windu: The Glᴀss Abyss reveals why Mace was the right pick for such a difficult time. We don’t know much about the years immediately before the prequels, but this reveals that Mace was tested by unseen conflict; he was likely picked in part because of prophecies from Jedi Master Sifo-Dyas, the Council Member who actually went rogue shortly before Star Wars: Episode I – The Phantom Menace and commissioned the clone army. But I think Mace had another role during the Clone Wars…

For Years, We’ve Been Getting Hints Of New Republic Black Ops

The Jedi Order is known to have conducted some clandestine black ops during the Clone Wars. The most obvious example is in Christie Golden’s fantastic novel Dark Disciple, which reveals a story originally planned for Star Wars: The Clone Wars ahead of its cancelation by Disney. This revealed that the Jedi Council sent Quinlan Vos on an undercover mission to ᴀssᴀssinate Count Dooku, one that involved an attempt to recruit Sith ᴀssᴀssin Asajj Ventress. It went badly wrong, with the two falling in love, and Quinlan even falling to the dark side for a while.

But he wasn’t the only one. Jedi: Survivor revealed the Jedi had undercover operatives such as Bode Akuna, who worked alongside Republic Intelligence. He even seems to have been taught some Force powers that were traditionally considered dark side, because he was able to conceal his presence in the Force, meaning other Jedi couldn’t detect him. There’s absolutely no reason to ᴀssume Bode was the only one of these agents.

There Were Also Elite Clone Commandos

The Jedi may have been running black ops, but there were other clandestine units in the running too. Clone Force 99 is the perfect example; a black ops unit who became something of a legend among the Grand Army of the Republic. As celebrated as Clone Force 99 may have been, though, their reporting lines were distinctly unclear; in fact, Hunter carefully avoided telling Anakin who issued his orders. Anakin explicitly asked him who he reported to in The Clone Wars season 7, episode 2, “A Distant Echo,” and Hunter answered simply: “Can’t say I’ve got an answer.“

Again, though, Clone Force 99 was not alone. They were one of many Clone Commando units, some chosen and some genetically engineered to possess unique skills and abilities that would help them operate in battle. Marc Sunerak’s The Secrets of the Clone Troopers – ostensibly reports from Captain Rex himself – claims that they “received enhanced training and augmented armor that placed them at a level high above the standard trooper.“

So here’s the question: who gave orders to these Clone Commando units during the war? They were part of the Special Operations Brigade, sometimes known as GAR Special Forces. In Legends, they were led by Jedi Generals Iri Camas and Arligan Zey, but neither of these are canon. In canon, curiously, several Special Forces missions have been led by Mace Windu himself.

We Now Know Mace Windu Issued Orders To Clone Force 99

Lucasfilm recently published preview pages for Star Wars: The Bad Batch – Ghost Agents #4, which tells the story of a Clone Force 99 mission during the Clone Wars. It’s easy to miss, but the biggest reveal is that Mace Windu is the one issuing orders to the Bad Batch. He’s clearly the one responsible for overseeing their operations – which makes a measure of sense. Mace is a skilled tactician, and he’d be the perfect choice to run clandestine operations. He was also tied to the Quinlan Vos mission among the Jedi, too.

But this raises an intriguing question: Why was Mace’s role kept secret? Hunter explicitly notes that he’s unable to tell Anakin who he normally reports to. The clear implication is that only the Jedi Council knew about the Special Forces missions… or, even more excitingly, that only Mace himself did. Mace skirted a lot closer to the dark side than other members of the Jedi Council, and – according to The Glᴀss Abyss – he was forged as a master through war. He’d be more comfortable with these operations than his fellow Councillors.

There’s A Side To The Clone Wars We’ve Never Really Seen Before

One thing is becoming abundantly clear; there’s a side of the Clone Wars that we’ve seldom seen. The Clone Wars animated TV show is primarily the tale of Jedi Generals demonstrating their heroism on the field of battle, accompanied by heroic clones who will ultimately be betrayed by the Sith when Palpatine activates Order 66. But there was another clandestine side to the conflict, one only hinted at in Dark Disciple and a few comics. A much darker story than the one we’ve ever seen on screen.

If I’m right, then Mace Windu was the one behind all these unseen black ops. We’ve seen the Clone Wars, but we haven’t seen Mace Windu’s war. This is a battle unlike any others, one fought in the shadows, with perhaps only the Jedi Council aware of it – and potentially not even them. Did these missions even get reported to Palpatine himself? If not, then the Emperor would have taken the throne with no knowledge of many secret missions. And Bode Akune proves how dangerous that could be for the Sith Lord.

Jedi: Survivor revealed some Jedi black ops operatives knew how to hide themselves from other Force-sensitives – the power that was key to Palpatine’s own success. The Bad Batch revealed some mutant and cybernetic Clone Commandos were resistant to Order 66, and Clone Force 99 may not be the only ones. Even worse for the Emperor, it’s entirely possible Mace Windu took these secrets with him when he died. This could explain why there are so many Order 66 survivors, and even fits with the Emperor’s decision to shut down the clone program. He had a lot less control than he thought.