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Star Wars: The Clone Wars’ final season gave fans the closure they needed when it came to Ahsoka Tano and Captain Rex’s journey. It also completed the task of finally linking The Clone Wars and Revenge of the Sith, which Dave Filoni’s planned, before its cancellation in 2013. 

But it didn’t answer one question: What happened to the Bad Batch after Order 66? Or even during the Jedi Purge? In the grand scheme of things, it’s not the biggest, more important mystery. But, this group of highly lethal clones, it would be interesting to know how they fared during this time. 

The Bad Batch, Rex, and Echo after their successful mission in 'Star Wars: The Clone Wars'
The Bad Batch, Rex, and Echo after their successful mission in ‘Star Wars: The Clone Wars’ | Disney+

When is the last time we see Clone Force 99/the Bad Batch?

The first arc of this highly-anticipated season introduced the Bad Batch, aka Clone Force 99. This is an arc that fans wanted since Filoni — supervising director and executive producer for the show — shared after the show’s cancellation. They are a group of mutated clones that go on special missions and can accomplish more than your average clone thanks to their “defects.”

These genetically mutated clones included Crosshair, who is an excellent sniper thanks to his modified eyesight. There’s also Wrecker, whose name says it all (he’s very strong and loves destroying things), and Tech, whose name is also self-explanatory (he’s the tech genius). The leader is Hunter, who has enhanced senses, which enables him to “hunt” any specific thing. In the last episode of the arc, Echo joins the group. Echo was a part of the 501st Legion, which is lead by Anakin Skywalker and what Captain Rex is a member of. The Separatists took Echo, turned him into a cyborg, and used him for his knowledge on Clone trooper maneuvers and know-how. 

The last fans saw of them, they rescued Echo, which took away the Separatists’ secret weapon. They successfully finished the mission, and Rex was all for Echo rejoining him and his brothers. However, Echo was such a changed man at this point and would fit in better with the Bad Batch. He stayed with them, and he and Rex had a bittersweet goodbye. 

The Bad Batch on their mission in 'Star Wars: The Clone Wars' Season 7
The Bad Batch on their mission in ‘Star Wars: The Clone Wars’ Season 7 | Disney+

‘The Clone Wars’: The Bad Batch Chose Their Name, Clone Force 99, To Honor a Fallen Brother

They were ‘defective’ or mutated, so did they have an inhibitor chip?

Since that’s the last we see of Clone Force 99, it’s hard to say what their involvement in Order 66 consisted of. If they did carry out Order 66, due to Palpatine’s orders and the clone’s inhibitor chips, they would have done a lot of damage. Normal clones were able to carry it out pretty successfully. So imagine what five enhanced Clone troopers could do? 

However, considering that they were mutated and defective in the eyes of the Republic, would the Kaminoans have taken out their chips? Would the chips have even worked on them with their different genetic makeup? It’s tough to say. 

On one side, it would have been smart on the Kaminoan’s part to keep the chips in, because if a powerful clone goes awol, you’d think that they’d want an “off” switch, so to speak. A way to mind control them if things got out of hand. 

On the other hand, the Bad Batch never followed traditional Clone trooper logic, protocol, or orders. They were a rogue team that still served under the Republic but were really in charge of their own unit. They didn’t serve under a Jedi General and went on special missions. It’s possible that their mutated state allowed for this and also made the chips nonessential. 

It’s hard to say which instance is more likely. Although, you’d think that if an elite group of Clone troopers was out killing Jedi, you’d hear about them more. They’d be a big anxiety for surviving Jedi and probably would have changed the game for the Empire. But again, if they weren’t a part of Order 66, what happened to them? Maybe fans will find out one day. 

Which Clone troopers did survive the chip and Order 66?

In Season 6, Fives found out about the inhibitor chip and also cracked the case about Palpatine being a bad guy which is way more than the Jedi did. He was able to give one last warning to Rex, although it was too late. It didn’t mean much to Rex then, but thankfully he recorded what happened and Ahsoka found it later on, when she was trying to escape Order 66. 

She removed the chip with the help of some lovely droids, which is how they both were able to survive the purge. We meet up with Rex again in Star Wars Rebels. And when we do, it’s revealed that Wolffe and Gregor also survived. 

Wolffe was a part of Plo Koon’s army of clones, but it isn’t revealed how or when he removed his chip. Gregor suffered serious brain damage after a crash following the Battle of Sarrish, which could have affected the chip’s control. Unfortunately, Gregor died during the Liberation of Lothal. Rex went on to serve the Rebel Alliance in the Battle of Endor.