As the residents of Station Square repair their city, GUN begins mass production of its own Hunter series robots to counter Dr. Eggman. Using a spy robot, Eggman examines their progress and notes with annoyance that "all they did was copy (his) designs." As he hacks GUN's computers for more information--displaying pictures of several GUN robots from Sonic Adventure 2--he finds a database entry for Gerald Robotnik. Eggman concludes that he was born on Earth, rather than in Sonic's world, and that the two are parallel dimensions. As Eggman continues his search, he uncovers Gerald's diary. Transferring it from GUN's computers alerts them to his activities, and the President assigns Rouge and Topaz to monitor him.
Rouge and Topaz secure a Chaos Emerald to use as bait to gain Eggman's trust--as well as the Master Emerald itself, which Rouge is unwilling to leave behind. Meanwhile, Eggman fights his way into GUN's base on Prison Island. He reaches the capsule containing Shadow and releases him, astonished to see the silhouette of a hedgehog in the cryogenic vapors.
The President's signature was visualy different in both America and Japanese versions.
Gerald Robotnik's diary was different in this episode than the one used in the source material, as it omitted any references to Maria's death or his resulting insanity, and in fact indicated that the main reason he wanted Shadow released was as vengeance against GUN for the measure of immorality he found intolerable in regards to a conspiracy involving taking over both his Artificial Chaos project as well as the Eclipse Cannon.
It also contained two swears, a rarity especially for the time this episode was released. This was omitted in the English dub, when every single word in the diary save for Project Shadow was replaced with dots.
Knuckles doesn't recognize Rouge in her costume. Even though it's the same costume she had on from episode 13, "Beating Eggman: Part 2 ".