The Genetic Pokémon Mewtwo served as the focal Pokémon for the second set, appearing as a Grade 5 Pokémon in the Mewtwo Course, one of the launch courses. Its counterpart, the New Species Pokémon Mew could be encountered on the same course as well, though much less frequently. Mew was also the first Pokémon Ga-Olé disk to have a collection number of "XXX". The Beginning Course acts as an introductory course, featuring relatively low-Grade Pokémon, including the Sinnoh first partner Pokémon, as well as some Pokémon from the first set.
A number of high-Grade Pokémon, including Xerneas, Yveltal, and Zygarde, could be encountered in the Zygarde Again Course, available to play from October. November saw the release of the Kyurem Course, in which the Boundary Pokémon Kyurem could be encountered as a Grade 5 Pokémon. The Greninja's Bond Course, available to play in conjunction with the release of Pokémon Sun and Moon in Japan, introduced a Grade 5 Greninja with the ability to transform into Ash-Greninja.
The second set also included some changes to game mechanics, including an increased capture rate across all Pokémon, and an increased encounter rate for Grade 4 and Grade 5 Pokémon. This change also increased the chances of a player encountering secret Pokémon, such as Shiny Pokémon. Conversely, the rate at which Fighting Spirit could be raised during gameplay was reduced. Another minor addition was the ability to give players a second opportunity to capture Pokémon after a failed attempt. Pokémon that did not enter the Get Chance state during a round and were not captured had a small chance to appear again in the following round, retaining the same HP.
A new game mode, Trainer and Battle (Japanese: トレーナーとバトル) was introduced with the launch of the second set, providing a similar gameplay experience to that of Challenge Battle from Pokémon Tretta. Trainer and Battle mode features 5 different Pokémon Trainers to battle against, each with a team of 4 Pokémon. Each of the Trainers have a difficulty rating based on the Grade of Pokémon in their team. Defeating a Trainer will earn the player a trophy, which can be retained if they have a Ga-Olé Pass. Trainer and Battle mode consists of a single round, and can only be won by defeating all of the opponent's Pokémon—if the round reaches the time limit, it still counts as a loss. Last Chance! follows the conclusion of Trainer and Battle mode as with Get by Battle mode, offering the player an opportunity to capture and dispense random Pokémon for an additional ¥100. Evolution Chance! and Grade Up Chance! will also follow the conclusion of Trainer and Battle mode if the player used any eligible disks.
Course summary
| Standard courses
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Zygarde Again Course ジガルデふたたびコース
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| Playable from October 6, 2016
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Kyurem Course キュレムコース
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| Playable from November 3, 2016
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Greninja's Bond Course ゲッコウガのきずなコース
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| Playable from November 18, 2016
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| Limited courses
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Available at participating stores with Pokémon Ga-Olé arcade units from September 15, 2016
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Sinnoh Setting Off Course シンオウたびだちコース
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| Playable from September 15 to December 7, 2016
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Available for Pokémon Ga-Olé Members to redeem from September 17, 2016 for 1,000 Member Points
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Mega Evolution's Power Course メガシンカのちからコース
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| Playable from September 17, 2016 to March 31, 2017
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Available as an insert in issue 50 of Pokémon Fan, released on September 20, 2016
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Water Types One After Another Course みずタイプぞくぞくコース
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| Playable from September 20 to December 7, 2016
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Special Mewtwo Course とくべつ ミュウツーコース
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| Playable from October 7 to 27, 2016 on select units
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Gible Outbreak フカマルたいりょうはっせい
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| Playable from October 20 to November 2, 2016
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Available as an insert in the December 2016 issue of CoroCoro Ichiban!, released on October 21, 2016
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Overthrow! Dragon Course だとう！ドラゴンコース
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| Playable from October 21 to December 7, 2016
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Trainer and Battle mode opponents
Fashionable Kid Chiemi
おしゃれキッズのチエミ
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| Difficulty: ★☆☆☆☆
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Hot-blooded Boy Yoshiaki
ねっけつしょうねんのヨシアキ
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| Difficulty: ★★☆☆☆
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Uniform Girl Rio
せいふくガールのリオ
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| Difficulty: ★★★☆☆
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Street Boy Shōgo
ストリートボーイのショウゴ
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| Difficulty: ★★★★☆
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Battle Leader Racto*
バトルリーダーのラクト
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| Difficulty: ★★★★★
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