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I know you can catch Celebi in Crystal VC but that's it

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Red and Blue:

The Nintendo 3DS Virtual Console releases can link with other Virtual Console Generation I and II core series games via Nintendo 3DS wireless communication, simulating the Game Link Cable. When initiating a link, the Virtual Console menu on the touch screen replaces the Cable Club attendant's dialogue.

Using Poké Transporter, Pokémon can be sent from the Generation I core series games to Pokémon Bank, from which they can be withdrawn in the Generation VII core series games.

The moves Blizzard, BubbleBeam, Confusion, Dream Eater, Explosion, Guillotine, Hyper Beam, Mega Kick, Mega Punch, Psychic, Reflect, Rock Slide, Selfdestruct, Spore, and Thunderbolt had their animations changed slightly to tone down the flashing.

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Gold and Silver

  • The Nintendo 3DS Virtual Console releases can link with other Virtual Console Generation I and II core series games via Nintendo 3DS wireless communication, simulating the Game Link Cable. Like in the original releases, they can only communicate with the Virtual Console Generation I core series games by using the Time Capsule. Unlike the VC releases of Generation I games, closing the communication normally does not cause the emulator to restart, although it does restart if the communication was cut due to an error. When initiating a link, the Virtual Console menu on the touch screen replaces the Cable Club attendant's dialogue. Additionally, all of the Game Boy Printer features are disabled, although the option still appears in the Pokédex and the PC menu.
  • Mystery Gift can be performed with other Virtual Console copies of Pokémon Gold, Silver and Crystal using the Nintendo 3DS system's infrared port. Unlike other link features, the user interface remains unchanged from the original games.
  • Using Poké Transporter, Pokémon can be sent from the Generation II core series games to Pokémon Bank, and from Pokémon Bank, they can then be moved to Generation VII core series games.
  • In battle, when a Pokémon attacks, its HUD doesn't disappear for the duration of the animation as it did in the original releases. This causes several graphical oddities, such as the animations of Tackle and Splash causing the user's HUD to move along with its sprite. Also, some moves had their animations changed slightly to tone down the flashing by dimming the screen, although this is not the case in all localized releases.
  • In the Japanese releases, Jynx's sprite has been replaced with the sprite used in Western versions, as the original had previously fell under controversy for its resemblance to blackface.

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Crystal:

  • The Nintendo 3DS Virtual Console releases can link with other Virtual Console Generation I and II core series games via Nintendo 3DS wireless communication, simulating the Game Link Cable. Like in the original releases, they can only communicate with the Virtual Console Generation I core series games by using the Time Capsule. Unlike the VC releases of Generation I games, closing the communication normally does not cause the emulator to restart, although it does restart if the communication was cut due to an error. When initiating a link, the Virtual Console menu on the touch screen replaces the Cable Club attendant's dialogue. Additionally, all of the Game Boy Printer features are disabled, although the option still appears in the Pokédex and the PC menu.
  • Mystery Gift can be performed with other Virtual Console copies of Pokémon Gold, Silver and Crystal using the Nintendo 3DS system's infrared port. Unlike other link features, the user interface remains unchanged from the original games.
  • Using Poké Transporter, Pokémon can be sent from the Generation II core series games to Pokémon Bank, and from Pokémon Bank, they can then be moved to Generation VII core series games.
  • In battle, some moves had their animations changed slightly to tone down the flashing by dimming the screen, although this is not the case in all localized releases.
  • In the Japanese release, Jynx's sprite has been replaced with the sprite used in Western versions, as the original had previously fell under controversy for its resemblance to blackface. In addition, due to the Mobile System GB not being present, Japanese players are unable to use any of the features in the Pokémon Communication Center, access the Battle Tower, and receive the Egg Ticket to exchange for the Odd Egg.
  • The event allowing the player to obtain the GS Ball and capture Celebi is activated by entering and leaving the Pokémon Communication Center (in the Japanese release) or the Pokémon Center in Goldenrod City (in non-Japanese releases) after entering the Hall of Fame, without any additional requirements. Not only is this event now available to Japanese players outside of set dates, and to worldwide players at all, it also occurs earlier in the game, as the original Crystal release required the player to get all eight Kanto badges first.

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