The title parallels Return of the Jedi.
3:32 - Clone pilot: "Set S-foils in attack position." Red Leader gives a similar instruction in A New Hope ("Lock S-foils in attack position" [1:45:38]), and so does Wedge in Return of the Jedi ("Lock S-foils in attack positions" [1:34:20]).
3:47 - Anakin: "This is where the fun begins." Han Solo has a similar line in A New Hope: "Here's where the fun begins" [56:26].
4:32 - Anakin (after a Vulture droid launches missiles at him and Obi-Wan): "Pull up!" Obi-Wan says this to Anakin during the speeder chase in Attack of the Clones ("Pull up, Anakin, pull up!" [17:08]); Biggs gives this instruction to Luke and to Porkins in A New Hope ("Luke, pull up!" [1:46:42] and "Pull up!" [1:47:22]); and Lando says it in Return of the Jedi ("Pull up! All craft, pull up!" [1:34:48]).
5:23 - Obi-Wan (after buzz droids land on his starfighter): "I'm hit!" In A New Hope, this is said by a Rebel pilot ("I'm hit!" [1:48:06]), Luke ("I'm hit, but not bad" [1:48:48]), and Wedge ("I'm hit!" [1:54:32]). A rebel pilot also says, "I'm hit!" in Return of the Jedi [1:44:16].
6:13 - Obi-Wan (after his cockpit window fogs over): "I can't see a thing." Luke says the same thing in A New Hope about his stormtrooper disguise ("I can't see a thing in this helmet!" [1:13:17]) and in The Empire Strikes Back while entering Dagobah's atmosphere in his X-wing ("All the scopes are dead; I can't see a thing" [41:09]).
6:26 - Obi-Wan (to Anakin): "You're gonna get us both killed!" Anakin says something similar to R2-D2 in The Phantom Menace: "R2, get us off this auto-pilot; it's gonna get us both killed!" [1:53:55], and Leia says something similar to Han in A New Hope, after he tries to shoot his way out of the trash compactor: "Put that thing away; you're gonna get us all killed!" [1:19:32]
6:30 - Obi-Wan (to Anakin): "Get out of here; there's nothing more you can do." Luke says something similar to Wedge in A New Hope: "Get clear, Wedge; you can't do any more good back there" [1:54:34].
7:24 - Obi-Wan: "Oh, I have a bad feeling about this."
10:22 - Battle droid (to Anakin): "Hands up, Jedi." A battle droid also says, "Hands up!" to Jar Jar and Captain Tarpals in The Phantom Menace [2:00:19], and storm trooper says, "Hands up!" to Han and Leia in Return of the Jedi [1:48:07].
11:49 - Anakin (to the Chancellor): "Are you alright?" In The Phantom Menace, Anakin asks Qui-Gon, "Are you alright?" [1:17:31] and Padmé asks Anakin, "You alright?" [1:19:06]. In Attack of the Clones, Padmé asks Anakin, "Ani, are you alright?" [50:02], and later a clone trooper asks Padmé, "Are you alright?" [2:05:54]. In A New Hope, Luke asks Obi-Wan this [59:16] and Biggs asks Luke [1:46:44], and in The Empire Strikes Back, Luke asks, "Rogue Two, are you alright?" [30:31]. Twice in The Empire Strikes Back, Han asks this with a shortened "You alright?" once to Luke [22:12] and once to Leia [31:39].
15:42 - Wilehlm scream (clone trooper)
18:43 - General Grievous: "General Kenobi, we've been waiting for you." Vader greets him similarly in A New Hope: "I've been waiting for you, Obi-Wan" [1:30:09].
19:12 - Grievous (to Anakin): "Jedi scum." Insults involving scum also appear in The Empire Strikes Back (Admiral Piett remarks, "Bounty hunters!? We don't need their scum." [1:05:52]) and Return of the Jedi (an Imperial officer says, "You rebel scum" [1:33:51]).
21:40 - Anakin (to Obi-Wan and Palpatine): "Strap yourselves in." Han Solo uses this same expression in A New Hope: "Go strap yourselves in; I'm gonna make the jump to lightspeed" [56:46].
24:38 - Anakin (to Obi-Wan): "Alright, but you owe me one, and not for saving your skin for the tenth time." Leia uses the same expression in A New Hope: "Somebody has to save our skins" [1:18:22].
24:53 - Mace Windu: "Chancellor Palpatine, are you alright?" See above, 11:49.
25:12 - Palpatine (to Windu): "And I assure you, the senate will vote to continue the war as long as Grievous is alive." As Emperor, he uses this same expression while talking to Luke in Return of the Jedi: "I assure you we are quite safe from your friends here" [1:32:08]. Qui-Gon also uses the expression in The Phantom Menace; after Queen Amidala says that Senator Palpatine fears the Trade Federation wants to destroy her, he replies, "I assure you I will not allow that to happen" [1:36:33].
26:12 - Anakin (after Padmé says, "There were whispers that you'd been killed"): "I'm alright." The circumstances are quite different, but Luke also says, "I'm alright" in A New Hope, after the scuffle in the cantina [47:21].
40:32 - Obi-Wan (to Mace, referring to Anakin): "With all due respect, Master, is he not the chosen one?" In The Phantom Menace, Qui-Gon and Obi-Wan's pilot uses the same expression: "With all due respect, the ambassadors for the Supreme Chancellor wish to board immediately" [2:06].
42:19 - Padmé (to Anakin): "Hold me." Leia also says this to Han in Return of the Jedi [1:22:17].
43:44 - Palpatine (to his entourage at the opera): "Leave us." As Emperor, he also says this in Return of the Jedi: "Guards, leave us" [1:30:55].
44:28 - Palpatine (to Anakin): "Search your feelings. You know, don't you?" Vader says the same thing to Luke in The Empire Strikes Back: "Search your feelings. You know it to be true." [1:51:26].
50:03 - As he jumps onto a Separatist tank, one of the Wookiees gives a Tarzan-like yell, which Chewbacca also does while swinging onto an AT-ST in Return of the Jedi [1:45:39].
51:13 - Obi-Wan (to Anakin, as Obi-Wan leaves for Utapau): "Goodbye, old friend." The phrase "old friend" is also used in Attack of the Clones (where Palpatine suggests "an old friend, like Master Kenobi" to protect Padmé [6:34] and Count Dooku calls Mace Windu "my old Jedi friend" [1:50:24] and just "old friend" [1:56:05]), in A New Hope (where Leia sarcastically says, "We, uh, ran into some old friends" when Han asks her and Luke where they've been [1:31:33]), in The Empire Strikes Back (where Yoda says that through the Force, Luke will see "Old friends long gone" [1:17:05]), and in Return of the Jedi (where Luke says, "I have a promise to keep to an old friend" [37:37] and Han calls C-3PO "an old friend of mine" [1:11:53]).
53:46 - Padmé: "I'm not gonna die in childbirth, Ani, I promise you."
Anakin: "No, I promise you."
In The Phantom Menace, Obi-Wan also makes a promise to Anakin: "You will be a Jedi, I promise" [2:07:43]
53:55 - This shot of Obi-Wan's starfighter exiting hyperspace, detaching from the hyperspace ring, and then flying to Utapau has the same basic composition and dynamic as the shot of his starfighter exiting hyperspace, detaching from the hyperspace ring, and then flying to Kamino in Attack of the Clones [40:54]:
57:30 - Obi-Wan (to Grievous): "Hello there." He greets R2 the same way in A New Hope [30:07].
1:07:28 - Obi-Wan (referring to the blaster he used to kill Grievous): "So uncivilized." It seems like this is meant to contrast with what he says about the lightsaber in A New Hope: "An elegant weapon for a more civilized age" [33:47].
1:16:32 - Palpatine (to Anakin): "The Force is strong with you." In a Jedi counsel meeting in The Phantom Menace, Ki-Adi Mundi says, "The Force is strong with him," referring to Anakin [1:33:06]. In A New Hope, Vader also says this about Luke (although he doesn't know it's Luke specifically, just a rebel pilot): "The Force is strong with this one" [1:55:41], and while talking to Vader in The Empire Strikes Back, Palpatine says, "The Force is strong with him," referring to Luke [53:46].
1:20:06 - The markings on the back of this battle droid bear a passing resemblance to 1138:
1:20:53 - Commander Cody (to a clone gunner, referring to Obi-Wan): "Blast him!" In A New Hope, Luke also yells this to Han, referring to the dianoga in the trash compactor: "Blast it, will you!?" [1:20:38]
1:23:40 - Jedi youngling (referring to the clones executing Order 66 at the Jedi temple): "Master Skywalker, there are too many of them." In The Phantom Menace, Captain Panaka says this about battle droids ("There are too many of them" [23:25]), and in Return of the Jedi, a rebel pilot says this about TIE fighters ("There's too many of them" [1:35:13]).
1:24:00 - C-3PO (to Padmé, about Anakin): "Don't worry; I'm sure he'll be alright." This is similar to what Obi-Wan says to R2 about Luke in A New Hope ("Oh, don't worry; he'll be alright" [30:17]) and what C-3PO says to R2 in The Empire Strikes Back ("Of course we'll see Master Luke again, and he'll be quite alright; you'll see!" [10:43] and "Don't worry about Master Luke; I'm sure he'll be alright" [12:45]).
1:35:06 - Palpatine (addressing the senate): "The attempt on my life has left me scarred and deformed, but I assure you my resolve has never been stronger!" See above, 25:12.
1:36:59 - Obi-Wan (to Yoda, as they're leaving the Jedi temple): "Wait, Master, there is something I must know." Luke says something similar in Return of the Jedi when he asks Yoda about Vader: "Yoda, I must know" [42:09].
1:38:44 - Obi-Wan (referring to Anakin): "Padmé, I need your help. He's in grave danger." First, Queen Amidala says the same thing to Jar Jar in The Phantom Menace ("I need your help" [1:37:55]), and Obi-Wan says this to Luke in A New Hope ("I need your help, Luke. She [Leia] needs your help." [36:03]). Second, Yoda uses the same phrase in The Phantom Menace when he tells Obi-Wan: "The chosen one the boy may be; nevertheless, grave danger I fear in his training" [2:06:38].
1:41:23 - Captain Typho (to Padmé): "As you wish, my lady." The phrase "As you wish" occurs a number of times in the original trilogy: in A New Hope, Vader says it after Tarkin asks him to release General Motti from his Force choke [38:45]; in The Empire Strikes Back, Boba Fett says it after Vader warns the bounty hunters against disintegrations [1:06:22]; in Return of the Jedi, Vader says it twice more in conversations with the Emperor [39:16 and 1:07:38], and Admiral Piett says it to Vader ("As you wish, my lord") [56:13]. In The Phantom Menace, Nute Gunray says, "As you wish" at the end of a conversation with Darth Sidious [5:04].
1:44:39 - Anakin: "I'm becoming more powerful than any Jedi has ever dreamed of." In Attack of the Clones, Count Dooku says something similar: "I've become more powerful than any Jedi" [2:08:30].
1:45:09 - Anakin (to Padmé): "And together, you and I can rule the galaxy." As Vader, he says something similar to Luke in The Empire Strikes Back: "Join me, and together we can rule the galaxy as father and son" [1:51:45].
1:59:23 - Anakin (to Obi-Wan): "You underestimate my power." In Return of the Jedi, as Vader, he says almost the same thing to Luke: "You underestimate the power of the dark side" [1:50:07].
2:09:21 - Obi-Wan (asking about Luke's future): "And what of the boy?" There are similarly constructed questions in A New Hope (General Tagge asks Tarkin, "And what of the rebellion?" [37:42]) and Return of the Jedi (Vader asks Palpatine, "What of the reports of the rebel fleet massing near Sullust?" [53:57]).
2:09:56 - Yoda (to Obi-Wan): "An old friend has learned the path to immortality." See above, 51:13.
2:13:33 - This shot of Owen, Beru, and Luke watching the sunset matches the shot of Luke watching the sunset in A New Hope [25:31]: