The main menu of the original version contains three options: "Play", "Learn", and "Extras".
In "Play" mode, the player can play a duel against a computer opponent, Julie, using one of four Half Decks, named Fighting Deck, Water Deck, Fire Deck and Xtra Deck. Initially, only the Fighting and Water decks are available. The additional two can be unlocked by typing the word "fire" on the main menu. Julie always uses the Fighting Deck, unless the player chooses it; in such case she uses the Water Deck. All four decks are composed of Base Set and Jungle cards.
The "Learn" feature is meant to teach about the mechanics of the Trading Card Game.
An "Academy Entrance Exam", with questions about the TCG, as well as about Pokémon in general. Finishing the test with 10/10 correct answers unlocks a certificate—which can be printed and taken to the Pokémon League, where it should be exchanged for "10 points in the Trainer's Badge Book"—a desktop wallpaper and a second, harder quiz. Finishing the second quiz unlocks another certificate (worth 20 points) and three additional wallpapers.
Two special issues of TopDeck (Wizards of the Coast's now-defunct magazine dedicated to TCGs), one with tips about the game and one focusing on the Pokémon League
Custom Pokémon Game Gear and coins to print
A video promoting the League
The wallpaper unlocked after beating the first quiz has a large Poké Ball in the center with Pikachu, Gengar, and Snorlax around it, on a blue background. Of the three wallpapers unlocked after the second quiz, one has a jungle background (reference to the expansion name) with Scyther in the center and Vileplume and Wigglytuff on the sides, another is supposed to look like a box with the Fossil set logo and Aerodactyl escaped out of it and the final one has a red background with Mewtwo on the left and a big Base Set 2 logo on the right.
The certificates are awarded for answering correctly 10 questions in a row, in the Pokémon Academy Entrance Exam.
It is not possible to put Pokémon on the Bench before the play starts. Instead, players must wait for their first turn to put Pokémon on the bench.
No Energy card is discarded from Magmar when using the Flamethrower attack. This issue was addressed in Version 2.