Lyman can be found throughout Part 1 at the Slifer Red dorm, but will refuse to duel or team up with the player unless Pharaoh is following them around.
During Part 2, Lyman partners with Fonda Fontaine. He mentions that they joined the Tag Force tournament as the faculty team, but laments being unable to partner with Pharaoh.
Weirdly, due to Lyman Banner and Amnael not being treated as the same character in Tag Force, partnering with Lyman throughout Part 3 will eventually lead to a Tag Duel against Amnael and Jaden Yuki. A similar oddity happens with Atticus Rhodes during the encounter with Nightshroud. However, if Amnael is the player's partner, Lyman is nowhere to be found during Part 2.
Lyman, as Amnael, appears in the Abandoned Dorm after 10:00 P.M during Part 1 if he was defeated during Part 3. Defeating him 10 times will result in Amnael awarding them with both of his Deck Recipes as well as 3 copies of "Alchemic Kettle - Chaos Distill"
If the player wants to partner with both Lyman and Amnael, they have to be asked separately during Part 1.
Tag Force 3
Lyman Banner and Amnael are now properly treated as the same character at all times.
During the last story event for Tier 2 and Tier 3 characters, the player and their partner Tag Duel against Amnael and Adrian Gecko. If the player is partnering with Adrian, they duel against Amnael and Jaden. If either Lyman or Amnael is the player's partner, Jaden teams up with Adrian.
Lyman, as himself, uses Decks focused on forcing players to payLife Points in order to perform actions while he uses a variety of effects to disrupt them and damage them further and to summon monsters in unusual ways, such as Tokens or Trap Monsters. Many of the cards he uses can be related directly or indirectly to alchemy, such as "Jar" monsters or mirror-themed cards like "Copycat" and "Reflect Bounder".
As Amnael, he uses Decks focused on removing cards from play.
Lyman does not use his second Deck, "Finite Entity", at any point during Story Mode. It can only be dueled against in Free Duel mode, and its Deck Recipe is given to the player upon beating Part 3 with Lyman as their partner.