While overseeing combat operations against Separatist raiders in the Outer Rim Zabrak Master Eeth Koth, was captured by General Grievous. Oki was present along with Ahsoka Tano, Barriss Offee, Finn Ertay, and numerous others in the Temple's communications room, when a holographic message from General Grievous arrived. In this message Grievous tortured the Jedi Master, and told the assembled Jedi that he didn't care about Republic and it's politics, he only wanted to see them all fall. The Jedi Masters, shocked and angry, told the others to take Padawans out of the room, while they discussed what should be done. Eekar Oki left the room with Finn Ertay, Ahsoka, Sora Bulq and some several Padawans.
The Republic-Separatist Negotiations
When Padme Amidala and Ahsoka Tano arrived on Raxus, capital of the Confederacy of Independent Systems, they met with Amidala's former mentor, Mina Bonteri, who had since joined Separatists. Together, they started Republic-Separatist negotiations with the goal of ending the Clone Wars, but Dooku had another plan, and thanks to Grievous, who destroyed the Senate District's main power generator on Coruscant. The negotiations stopped, but Oki, who found out that Ahsoka and Amidala stowed away on a transport bound for the Confederate capital, Raxus, told Anakin, who was angry at them, and told them that they crossed the line.
Talking with Younglings
When Ahsoka, O-Mer, and Jinx arrived at the Jedi Temple after they were held as prisoners by the Trandoshans, Eekar Oki met with them and listened to youngling's story about Trandoshan huntings and more.