Despite being a pure fighting game, Pokkén Tournament has got a nrrative that flows through the Single Player mode, Ferrum League. This page details the main encounters, although some trainers you face will mention bits between battles.

Encounter #1: Green League
League Beaten: Green League
Shadow Mewtwo HP: 1000
Loseable?: Yes
Support Pokémon Usable: Yes
Synergy Burst Usable: Yes
Stage: Dark Colosseum

Details:
After beating Travis in the Green League, a trainer suddenly appears and challenges you. This is the first fight against Shadow Mewtwo. After completion of the battle, win or lose, Nia and Travis discuss what happened and how there have been rumours lately about a mysterious black Pokémon. This is the full extent of your first encounter

Encounter #2: Blue League
League Beaten: Blue League
Shadow Mewtwo HP: 1000
Loseable?: Yes
Support Pokémon Usable: Yes
Synergy Burst Usable: Yes
Stage: Dark Colosseum

Details:
After beating Keith in the Blue League, the story continues. The mysterious trainer and her Mewtwo appear again, saying they sensed the power coming from the two of you. Nia notes that the stone is sucking up Synergy Power and the next battle commences. Once the battle is complete, Nia notes that it was sucking up Synergy Power and speculates that the trainer and her Mewtwo may have been looking for you.

Encounter #3: Red League
League Beaten: Red League
Shadow Mewtwo HP: 1000
Loseable?: No
Support Pokémon Usable: Yes
Synergy Burst Usable: Yes
Stage: Dark Colosseum

Details:
After beating Elinn in the Blue League, the story continues once again. The mysterious trainer appears and wonders if you can achieve Synergy with Mewtwo. After this, Mewtwo challenges yet again. This time, the battle has to be won. When defeated, Mewtwo starts sucking in all the Synergy Energy from the nearby Synergy Stones and absorbing all the Gaia Power. The mysterious trainer asks you to save Mewtwo and for your help.

Encounter #4: Synergy Stone Power
League Beaten: Red League
Loseable?: No
Support Pokémon Usable: No
Synergy Burst Usable: Yes
Stage: Regi Ruins

Details:
After the encounter with Shadow Mewtwo, the Ferrum League has been put on hold until they work out the issues with the Gaia Power as Pokémon can't use Synergy Burst anymore. The trainer identifies herself as Anne and explains that the Shadow Synergy Stone is influencing Mewtwo. The Shadow Synergy Stones are said to be the opposite of standard Synergy Stones. Explaining Synergy Power, she mentions that Shadow Synergy Stones absorb Synergy Power and that Mewtwo has merged with the Shadow Synergy Stone. Anne has tried to control the power but asks for your help to stop Mewtwo

After this, a Special Event area opens up in the Regi Ruins where Anne introduces Walter, one of her people and discuss the issues being faced. Walter asks if Anne has a special brooch which is a fragment of a Synergy Stone. He mentions a historical event where the Synergy Stone in the broach once quelled the Shadow Synergy Stone in the past, last time this happened. He says that the stone can regain the power in order to stop the Shadow Synergy Stone and by achieving Synergy with Mewtwo, it can be stopped.

To do this, a battle begins against Walter and his Gengar within the Regi Ruins. Defeat Walter and he sees that you have potential, but that the brooch has not yet recovered, and sends you to face off against other people to help restore it.

Encounter #5: Nora's Test
League Beaten: Red League
Loseable?: No
Support Pokémon Usable: Yes
Synergy Burst Usable: No
Stage: Blue Dome

Details:
The next encounter is to the south east of Ferrum in the Blue Dome where Nora is encountered. She mentions about how Gaia power is draining there. Then, combat is challenged and in this match, Synergy Burst cannot happen as Nora suggested it make the battle interesting, though Anne states that it isn't the time for it. The battle is against Nora's Gardevoir.

Defeat Nora and the brooch will regain more strength, but not be near enough, as the Shadow Synergy Stone's power is increasing.

Encounter #6: Jake's Test
League Beaten: Red League
Loseable?: No
Support Pokémon Usable: Yes
Synergy Burst Usable: No
Stage: Dragon's Nest

Details:
The next encounter is to the north east of Ferrum in the Dragon's Nest where Jake meets up with you. He wants the details, but the battle has to commence first. This battle is against Jake's Lucario, has no Synergy Burst, but allows for Support Pokémon.

Once defeated, the brooch is almost ready to take the Shadow Synergy Stone, but it's too late. The planet has lost too much Gaia Power, so the battle has to commence immediately.

Encounter #7: Final Synergy
League Beaten: Red League
Loseable?: No
Support Pokémon Usable: Yes
Synergy Burst Usable: Yes
Shadow Mewtwo HP: 3000
Stage: Dark Colosseum (Final)

Details:
The next encounter is to the north east of Ferrum and has you finally face up against Shadow Mewtwo. Set your Support Pokémon ahead of time. As you discuss it, you find Mewtwo nearby and the Brooch reacts to the Shadow Synergy Stone which weakens it and allows you to get start battling Mewtwo.

In the first round, there's no synergy Burst usable, and Anne asks for you to keep Mewtwo under control. Round one has to be won. In the second round, Mewtwo starts being able to Synergy Burst, and its power spikes. This prevents you from being able to do any damage to it. Round two has to be lost.
For the final round, Anne manages to give you maximum Synergy Power, giving you permanent Synergy Burst to be able to take on Mewtwo once and for all. Win Round 3 and the battle is done. The brooch will cause the Shadow Synergy Stone inside Mewtwo to shatter. and Mewtwo returns to normal.

Encounter #8: End

Details:
As the battle ends, the brooch will cause the Shadow Synergy Stone inside Mewtwo to shatter. and Mewtwo returns to normal and the Shadow Synergy Stone is separated from it once and for all. The brooch has shattered and Anne notes that it's because of you that Mewtwo was able to be saved. Anne leaves and takes the Shadow Synergy Stone back to her people.

Mewtwo is now unlocked for play and the Ferrum League can be rejoined for the Chroma League.

After you have beaten the Chroma League, and unlocked Shadow Mewtwo as a playable character, the Special Events in this are able to be replayed at will.

 
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