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This episode shows that you don't need a hand to use the force. When Anakin uses the force choke on the seperatist member, he is using his handless arm.
When the recently mutated Nelvaanian runs towards Anakin and pulls off the mind-control device on the Nelvaanian, his machine-hand gun disappears.
In Attack of the Clones, Anakin's arm is cut off halfway between the shoulder and elbow, but in this episode the robotic arm is halfway down the forearm.
When Anakin is walking through the cave, at one point his scar (as well as the blue marking that was covering it) disappear.
Yoda's mount from Episode 1 reappears. It makes the same sounds as the Tauntauns from The Empire Strikes Back.
If you look closely enough, Padmé appears to be pregnant with Luke and Leia.
The two Jedi who assist Shaak-Ti in escorting Chancelor Palpatine to safety are of the same species of aliens who appeared in the bar scene at Mos Eisley in A New Hope.
When Saesee Tiin landed on the enemy's ship, he cuts a hole with his lightsaber and uses the Force to throw it away, but when he goes down, the hole is pushed down.
Though not stated in the episode, Anakin's scar is the result from a rematch with Asajj Ventress, from the graphic novel Star Wars: Clone Wars - Volume 6.
The first three scenes of Anakin fighting across the galaxy take place two years and three months afther Attack of the Clones.The third scene where he returns with the scar is about a month after that. The rest of this chapter, along with "Chapter XXIII," "Chapter XXIV," "Chapter XXV," take place in the month leading up to Episode III (two years and eleven months after Episode II).
The trade federation General shown in the beginning is most likely "Pors Tonith," banker-turned-admiral from the novel Jedi Trial.
A clip from The Phantom Menace is used in this episode, but it's animated.
This is the first time Mace Windu speaks in this mini-series. Also the first time Jedi Council members Even Piell, Eeth Koth, Adi Gallia, Kit Fistu, and Oppo Rancisis speak in any setting.
When C-3PO delivers Anakin's Padawan braid to Padmé, she places it in a small box. If you look inside the box you'll also see the necklace Anakin made for Padmé in The Phantom Menace as keepsake. That means she actually saved it for all those thirteen years.
Yavin 4 (specifically the abandoned temple that is briefly seen here) was the location of the Rebel Base in A New Hope.
Even though Padme is not a Jedi, Yoda apparently trusts her enough to tell her that his mission involved a secret Jedi Temple. Could it be possible that Yoda feels a sort of paternal bond towards Padme like he eventually will towards Luke?
In this episode, we see the making of a lightsaber. There was a diagram, once, in Time magazine, of what the inside of a lightsaber looks like, and, sure enough, there was a special-colored crystal inside.
Jedi Master Luminara Unduli and Padawan Barriss Offee were two of the Jedi in the climactic battle in Attack of the Clones.
There is a Republic symbol on the top side of the piston.
In the movie, Attack of the Clones, dozens of Jedi can't stop a droid army. Yet, Mace Windu, who was present at Geonosis, was able to force push a droid army twice the size of the Geonosis Army, out of the way.