Misty's Staryu uses BubbleBeam for the first time.
The Mewtwo from Mewtwo Strikes Back and Mewtwo Returns is mentioned by Dr. Yung.
Misty has a pink bag in this special.
Professor Oak now has a Dragonite.
In this special Pikachu knows Volt Tackle. However, James received Mime Jr. prior to Pikachu learning Volt Tackle, and that pokémon is noticeably absent from this special episode.
The re-dubbed version of this special (not the one that aired on TV) is available on DVD packaged together with the eighth movie Lucario and the Mystery of Mew.
Scenes from Pokémon The Movie 2000, Pokémon 3: The Movie, Pokémon 4Ever, and Pokémon Heroes are seen when Mirage Master is scanning Pikachu's memory.
Tracey, Professor Birch, and Professor Elm make cameo appearences.
When this special aired in the US, the episode were Pikachu learns Volt Tackle hadn't aired yet.
This episode celebrates the 10th Anniversary and eight years of the Pokémon anime.
The way Mewtwo attacked (with the heads of other Pokémon appearing on it's body) is somewhat similar to what happened in Digimon, where Apacolymon attacked almost in the same manner.
The Mirage System Generators are very similiar to the Dimensional Area Generators from MegaMan: NT Warrior.