In Part 1 of Yu-Gi-Oh! GX Tag Force, the player can attempt to allow Zane to be selected as a partner for the Tag Force tournament in Part 2. Upon getting his heart level to full, he gifts the player with a "Power Bond" card. During Part 2, he partners with Syrus during the Tag Force tournament if not partnered with the player. During Part 3, he will Duel the player and their partner alongside with the Shadow RiderCamula. He is returned to normal upon defeating him. After the player defeats Kagemaru, he compliments the player for winning the duel.
On a side note, Yu-Gi-Oh! GX Tag Force uses a custom September 2006 Banlist, and as such does NOT limit Future Fusion nor Overload Fusion. Despite this, Zane never uses Overload Fusion and only uses Future Fusion in Part 2 (and when selected as a Partner), thus greatly limiting his power, since this OTK combo is considered to be the most powerful deck in this game by many.
Zane uses this Deck during the first half of Part 1.
Underworld is still primarily based on his Cyber Dragon cards and its Fusion Monsters. During Story Mode, Zane will duel the player with this Deck before the player reaches their Fourth Heart Event with their partner. When selecting Zane as a partner, he will use this Deck to duel along with the player (even when choosing normal Zane).
Underworld Rev is Zane's first Deck to branch into using Cyberdark Dragon and itsFusionMaterials. As such, the Deck also commandeers Dragon-Type Monsters for the Cyberdark monsters to use their effects. During Story Mode, Zane will duel the player with this Deck after the player has completed their fourth Heart Event with their partner.
Underworld Forb is a very powerful Deck that compiles all of Zane's Cyberdark Dragons used in Underworld Rev with his Chimeratech Overdragon. During Story Mode, Zane will duel the player with this Deck if the Deck the player is currently using contains a Forbidden card(s).
Message to All, in contrast to the other Decks, basically revolves around Cyber Dragons that Normal Zane would typically use. During Story Mode, Zane uses this Deck only in the flashback to the Graduation Duel in Jaden Yuki's fifth Heart Event.
Underworld Ult is another take on Zane's Cyberdark Dragons although his Cyber Dragon Fusions are still present. During Story Mode, Zane will use this Deck only during Syrus Truesdale's eighth Heart Event.