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If you chose the Republic, Anakin and Ahsoka are in the Y-Wing starfighter. Droids attack them and Anakin uses the force to transform part of the Y-Wing into a rocket. Ahsoka is then put in the rocket and is launched out into space. Anakin is then captured by a Separatist Shuttle. ARC-170 starfighters then come to defeat the droids. Anakin is then freed from the clones. The Y-Wing and ARC-170 starfighters head to a venator-class republic attack cruiser.
If you chose the Separatists, Anakin is captured by Nute Gunray and put in a electric-force generated chamber. Nute Gunray tries to get evidence out of Anakin but fails to do so. Anakin and R2-D2 are freed from the clones.