The Clone Wars - S3E21 - "Padawan Lost"

1:36 - Anakin (to Ahsoka):  "Don't get cocky."  In A New Hope, Han says this to Luke after he shoots one of the Death Star's sentry ships:  "Great, kid!  Don't get cocky." [1:35:27].

3:15 - Anakin (to the clone troopers):  "Steady, steady.  Wait for my move."  In The Phantom Menace, Jar Jar also says, "Steady, steady" (but to the Gungan soldiers) [1:48:30].

5:02 - Anakin: "Where could she [Ahsoka] be?"  Luke has a similar line in A New Hope as he's trying to raise C-3PO on his comlink:  "Where could he be?" [1:22:12 and 1:23:19], and C-3PO himself has a similar line a bit later in A New Hope:  "Where could they be?" [1:29:33].

12:23 - Jinx (to Ahsoka):  "There were other Padawans here that once thought as you do now."  This bears some similarity to what Vader says to Luke in Return of the Jedi:  "Obi-Wan once thought as you do" [1:24:48].

20:12 - Kalifa - "Please, Ahsoka, leave me."  As he's dying, Anakin says basically the same thing (to Luke) in Return of the Jedi:  "Now, go, my son, leave me" [2:00:45].

The Clone Wars - S3E20 - "Citadel Rescue"

1:04 - Anakin:  "We're gonna have to fight our way off this rock."  In A New Hope, Luke disdainfully refers to Tatooine using the same expression; after C-3PO asks if there's anything he can do to help, Luke replies, "Not unless you can alter time, speed up the harvest, or teleport me off this rock" [19:58].

3:15 - Sobeck (to Dooku, about the hyperspace coordinates):  "I will see to it that they are soon back in our possession."  While the specific diction is a bit different, Vader says something similar in A New Hope during a meeting on the Death Star:  "The plans you refer to will soon be back in our hands" [37:52].

4:00 - In the background of this shot, Commander Cody jumps on top of a crab droid and fires his blaster into it.  In Revenge of the Sith, an-other clone trooper does the same thing [1:20:01].

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6:34 - Anakin (to Ahsoka, discussing the Jedi's role in the war):  "But we aren't soldiers; we're peacekeepers."  Mace Windu also says this in Attack of the Clones, although slightly differently:  "We're keepers of the peace, not soldiers" [4:49].

6:49 - Ahsoka:  "Did you hear that?"

Even Piell:  "Yes, we're going to have company."

Both of these lines also appear in A New Hope.  At the beginning of the movie, C-3PO asks R2-D2, "Did you hear that?" [2:47] (incidentally, this is the first line of dialogue), and later, Han yells, "Luke, we're gonna have company!" [1:15:46].

7:13 - Sobeck:  "Tighten your grip, K2-B4."  Leia uses this same expression in A New Hope:  "The more you tighten your grip, Tarkin, the more star systems will slip through your fingers" [57:44].

12:35 - Sobeck:  "I will deal with this personally."  It's probably coincidental, but this seems to combine Grievous' line "I will deal with this Jedi slime myself" in Revenge of the Sith [58:03], Vader's line "See to it personally, commander" in A New Hope [8:42], and Vader's "I will deal with them myself," referring to the Rebel strike force, in Return of the Jedi [56:10].

16:05 - Wilhelm scream (Clone trooper)

20:36 - There's a brief musical cue of the Imperial March as Tarkin and Anakin shake hands.

The Clone Wars - S3E19 - "Counterattack"

3:17 - Count Dooku:  "You may cease the propriety, Commander Sobeck."  Vader says basically the same thing (to Moff Jerjerrod) in Return of the Jedi:  "You may dispense with the pleasantries, commander" [3:58].

15:26 - Anakin (to Rex):  "Throw me a charge."  Han Solo says the same thing in Return of the Jedi:  "Throw me another charge" [1:51.25].

The Clone Wars - S3E18 - "The Citadel"

4:55 - Fives (about being carbon frozen):  "Are, uh, we sure this thing is safe?  I don't want to end up a wall decoration."  In A New Hope, C-3PO also asks this (to R2 about the escape pod):  "Are you sure this thing is safe?" [7:18].  The "wall decoration" part is a reference to what later happens to Han Solo in Return of the Jedi.

6:52 - Tactical droid K2-B4 (to the Republic's re-programmed battle droid):  "What is your cargo?"  In Return of the Jedi, Admiral Piett asks a similar question:  "Shuttle Tydirium, what is your cargo and destination?" [55:27].  More generally, the whole situation of sneaking into enemy territory in a stolen ship is similar.

The Clone Wars - S3E17 - "Ghosts of Mortis"

1:45 - Ahsoka (speaking about the Jedi shuttle):  "After that, I have no guarantees she'll hold together."  In A New Hope, Han Solo (referring to the Millennium Falcon) uses the same expression:  "Don't worry; she'll hold together" [1:34:57].

3:29 - Father (to Anakin):  "Do not underestimate my son."  Warnings against underestimation occur twice in Return of the Jedi.  Luke tells Jabba, "It's your choice, but I warn you not to underestimate my powers" [24:26], and later Yoda tells Luke, "Luke, do not, do not underestimate the powers of the Emperor" [43:31].  In The Phantom Menace, Nute Gunray advises a battle droid, "These Jedi are not to be underestimated" [10:43], and in A New Hope, Vader tells Tarkin, "Don't underestimate the Force" [1:16:33].

5:25 - Qui-Gon:  "Remember your training, Anakin:  trust your instincts."  This is similar to what he tells him in The Phantom Menace:  "Feel, don't think; use your instincts" [57:47].

8:08 - Father (to Obi-Wan):  "You cannot interfere!"  This is similar to what Obi-Wan says to Luke in The Empire Strikes Back:  "If you choose to face Vader, you will do it alone.  I cannot interfere." [1:24:25].

9:25 - Anakin's vision of the future includes Obi-Wan's "You were my brother, Anakin" from Revenge of the Sith [2:00:25], Vader's "I hate you" from Revenge of the Sith [2:00:15], and the Death Star's destruction of Alderaan from A New Hope [59:05]:

10:20:  Son:  "Join me, and together we will destroy this emperor you see in your vision, and we shall end war, corruption, and suffering throughout the galaxy."  As in the previous episode, there's a resemblance between this line and what Vader says to Luke in The Empire Strikes Back ("Join me, and I will complete your training" [1:50:39] and "Join me, and together we can rule the galaxy as father and son" [1:51:45]) and what Dooku says to Obi-Wan in Attack of the Clones ("You must join me, Obi-Wan, and together we will destroy the Sith!" [1:33:07]).

11:50 - Anakin (to Obi-Wan):  "You will try to stop me."  In Revenge of the Sith, after Obi-Wan says, "I will do what I must," Anakin replies with a similar line:  "You will try" [1:47:46].

13:43 - Ahsoka:  "Mm, nice job."  She says this about Obi-Wan's progress in climbing out of a chasm.  It's a bit unclear whether she means this genuinely or sarcastically, but if it's the latter, there's a resemblance to Obi-Wan's sarcastic "Good job" about Anakin and Padmé's attempt to rescue him in Attack of the Clones [1:45:00].

20:07 - When the Father dies, he disappears in the same way that Yoda does in Return of the Jedi [45:07].  Obi-Wan's death in A New Hope [1:32:22] is similar but occurs in between shots, not within a single shot.

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Starting around 8:33 during Anakin's conversation with the Son, there's a brief musical cue that's similar to "Battle of the Heroes" from Revenge of the Sith, and there are musical cues of the Imperial march at the end of Anakin's vision and at around 11:44 when Anakin talks to Obi-Wan.