Rex and Jesse watch in astonishment as the Bad Batch single-handedly dispatch the entire force with their unconventional tactics. Their crash site is soon discovered by a large force of Droids, but Hunter and the Bad Batch insist on taking them head-on. As they enter approach the Separatist cyber station, their gunship is shot down by enemy fire, severely injuring Cody in the crash. Their genetic mutations and brash attitudes are a source of mistrust and conflict between themselves and the regular clones, but Cody convinces them to work together on this mission.

Rex recruits ARC Trooper Jesse and medic Kix while Cody enlists the help of an experimental Clone Commando squad, Clone Force 99. Windu then tasks Cody and Rex to take a squad to infiltrate the Separatist cyber station on Anaxes and confirm their suspicions. However, he confided the algorithm with only two of his men, Fives and Echo, the latter of whom was presumed dead at the Citadel.

Trench possesses an algorithm for the Republic's battlefield strategies, which was developed by Rex in the interest of reinforcing their weaknesses. Commander Cody and Captain Rex arrive at the command center, where Rex explains his theory as to why the Confederate commander of the battle, Admiral Trench, is able to counter the Republic's advances so effectively. The mounting losses indicate that the Republic is fighting a losing battle. At the Republic base, Jedi General Mace Windu confers with Anakin Skywalker that the Separatists have overrun their main facility.

The clones look to uncover the source of the Separatists' strategies.and bring in an elite squad called the Bad Batch.Ī fierce battle rages on the planet Anaxes and the Separatists have gained the advantage. Rex, Cody, and Clone Force 99, an unorthodox, elite squad also known as the Bad Batch, look to recover the Republic's strategy algorithm from Admiral Trench.

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