Grievous tábornok vakmerő támadást indít a kaminoi klónközpont ellen. Egy leselejtezés előtt álló klónszakaszra vár a feladat, hogy megmentse a helyzetet.

The Republic learns of an impending Separatist attack on Kamino, and Anakin and Obi-Wan hurry to the planet. After the Republic repulses the Separatists' diversionary assault, the real attack begins. Asajj Ventress, General Grievous and an army of droids rise out of the oceans, bent on destroying Kamino's clone production facilities. Rex, Cody, Fives, and Echo lead the clones in a desperate defense of their home planet.

Ryloth is under siege. Trapped on the surface, Jedi Master Di rallies the local forces with the help of Cham Syndulla. Desperate to save them, the Jedi Council dispatches Senator Bail Organa and Representative Jar Jar Binks to the planet Toydaria, where they are to convince the neutral regent, King Katuunko, to send aid to Ryloth. Bail and Jar Jar must convince Toydaria that their cause is just -- before it's too late. Trade Federation envoy Lott Dod attempts to prevent the Toydarians from giving up their neutrality. Katuunko follows his conscience and secretly aids the Republic, which Jar Jar is able to keep secret from the snooping Trade Federation agents with his inimitable distractions.

A militarista Pantora-hold szenátorának, Papanoida bárónak a lányait elrabolják. A tettes Greedo, a rodiai fejvadász. A nyomok előbb Jabbához, majd (miután a hutt maffiavezér ártatlannak, sőt korrektnek bizonyul) a Kereskedelmi Szövetség felé vezetnek. A báró személyesen vezeti a nyomozást.

A Mandaloron újra felütötte fejét a bűnözés, amely, mint kiderül, már a kormányőrséget is megfertőzte. Egy csapat testőrkadét, miközben leleplez egy botrányt, halálos veszélybe kerül.

Ahsoka is assigned to teach a class at a leadership academy on Mandalore. Soon after she arrives, Duchess Satine's zealous nephew -- Korkie -- and his classmates uncover a nefarious plot. Prime Minister Almec is revealed to be an active part of the black market conspiracy on Mandalore, and he attempts to permanently silence Duchess Satine and the cadets before they expose his corruption. Ahsoka and the cadets defeat Almec before he can succeed.

In the middle of a routine shopping trip on Coruscant, C-3PO is abducted by the bounty hunter Cad Bane. Bane is looking for information about the Senate building on behalf of Jabba the Hutt. Finding C-3PO devoid of useful information, Bane and his accomplices kidnap R2-D2 and extract the vital data, before memory-wiping the droids of the incident, and letting them on their way. The floor-plans and security details of the Senate building are part of a plot engineered by the Hutt families to free their imprisoned brother, Ziro the Hutt, who holds potentially damaging information about Hutt activities.

Cad Bane és Obi-Wan Quinlan Vos-szal társulva versenyt futnak, hogy elkapják a Hutt bűnözőt, Ziro-t, aki felbérelte Singet Amidala szenátornő ellen.

Az epizód főleg Ahsoka személyére koncentrál. A Palpatine kancellár elleni szervezkedés a szenátorok körében egyre komolyabbá válik, a pacifistává lett Amidala szenátor titkos és illegális találkozót bonyolít le a szeparatisták békére vágyó szárnyának legjelentősebb alakjával, a raxuson élő Mina Bonterivel, a szeparatista Onderon szenátornőjével. Az epizód cselekménye a negyedik évad A Friend in Need c. részében is folytatódik.

Padmé, Bail Organa and Onaconda Farr attempt to rally Senators in opposition to a bill that would appropriate funds for millions of new clone troops and have disastrous financial consequences for the Republic. Their opposition to the measure, however, soon makes them targets for intimidation and attacks by hired guns. After escaping two hired thugs -- Chata Hyoki and Robonino -- in a harrowing speeder bike chase, Padmé is able to sway the Senate with a stirring account of how the war has affected an everyday civilian, her handmaiden Teckla Minnau.

Dooku gróf Palpatine parancsára elcsapja tanítványát, Asajj Ventresst, mert a nő ereje túlságosan nagyra nőtt. A szakítás nem békés és Ventress kis híján meghal. Anyabolygójára, a Dathomirra menekül, ahol népe, az éjnővérek, valamint a nekik alávetett zabrakok élnek. Ventress bosszút forral Dooku ellen.

Dookunak új tanítványa lesz: Savage Opress, egy könyörtelen zabrak harcos. Egyikük sem tudja, hogy Opress csupán Ventress bosszújának eszköze.

Dooku kiképzésének első lépcsője a Ventress által felkutatott zabrak bérgyilkos-tanítványon a befejezéshez közelít. A jedik megkezdik a devaroni mészárlás végrehajtója utáni keresést.

A mysterious force draws Anakin, Obi-Wan and Ahsoka to a distant planet, and its inhabitants -- a family of exceptionally powerful Force-wielders -- in an attempt to determine whether Anakin is truly the Chosen One. The patriarch of this family, known only as the Father, has spent ages maintaining the balance between his Daughter, who is strong with the light side of the Force, and his Son, who aligns with the dark. The Father reveals his days are numbered, and he seeks Anakin to take his place as the fulcrum of this balance. A series of tests proves that Anakin is capable of controlling both offspring, as the Father does, but Skywalker refuses to take the Father's place.

Mielőtt a Jedik elhagyhatnák a Mortis-t, a Fiú elrabolja Ashoka-t, hogy megpróbálja Anakin-t átállítani. Anakin-nak az Atyá-val és a Leány-nyal kell egyesíteni az erejét, hogy legyőzzék a Fiú-t. Eközben a Fiú egy sötét mágiával átállítja Ashoká-t a sötét oldalra.

A Jedi-k Mortis-on rekedtek, a Fiú egyre erősebb a sötét oldalban és Anakin-t próbálja most átállítani. Anakin megdöbbent, amikor meglátta a sötét jövőt. A Fiú azt ígéri ha mellé áll, akkor együtt elháríthatják ezt a végzetet.

With help from R2-D2 and a squad of captured battle droids, an elite team of Jedi and clone troopers led by Obi-Wan and Anakin attempt to free a captive Jedi general, Even Piell, from an impenetrable prison. Despite orders to the contrary, Ahsoka Tano tags along, though she proves indispensable when the infiltration mission begins to evolve. Piell and his fleet officer, Captain Tarkin, are liberated from their cells, but now the fugitives must escape the Citadel itself.

With freed prisoners in their possession and the brutal warden attempting desperately to thwart them, Obi-Wan and Anakin search for a way out of the Citadel and back to Coruscant. The prison, however, has more traps, perils and pitfalls in store for them than they had imagined and they must work past their differences if they are to escape. Their bid to board their shuttle fails when heavy weapons fire destroys the escape craft. Trooper Echo dies in the blast. The escapees then flee to the caves and call for rescue from the Jedi Temple on Coruscant.

After their ship and only way off the planet is destroyed, Anakin and Obi-Wan must lead the escaped prisoners across Lola Sayu's perilous landscape as Plo Koon commands a task force of four cruisers and their fighters through the Separatist defenses in a daring rescue. Even Piell is ravaged by anooba tracking beasts, but before he dies, he passes on his Nexus Routes coordinates to Ahsoka. When the survivors return to Coruscant, Ahsoka knows half the intel, and refuses to disclose it to anyone but the Jedi Council, while Tarkin refuses to hand over his half to anyone other than the Chancellor.

Egy szeparatista erőd ostroma közben Ahsoka nyom nélkül eltűnik. Egy trandosán kolónia fogságába kerül számos más áldozattal együtt, ahol fogságba ejtőik sportból életre-halálra vadásznak rájuk. Anakin kétségbeesetten keresi a padawanját, ám annak magának kell kimásznia a bajból.

As Ahsoka and her youngling allies struggle to evade the Trandoshan hunters, their efforts receive an unexpected boost when a new captive -- Chewbacca the Wookiee -- arrives. Chewie scrounges parts from a wrecked Trandoshan slave ship, assembling a communicator to send out a distress signal. Help arrives in the towering, shaggy form of Wookiee warriors led by General Tarfful. Freed from captivity, Ahsoka returns to the Jedi Temple and is reunited with Anakin Skywalker.