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so its really confusing, with the comatose chespin, and the machine that makes Z2 obey team flare, and the mega evolution energy, and the chespin being in the weapon zygarde thing and negative energy and arggh

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That was a different Chespin than the one Clemont has if you don't know. Watch the (4? 5?)-part mega-evolution special to understand the plot better.
I know that filler
It isn't filler if it's important to the story.
no, i typed filler because you need filler in a comment to post it, sorry it should be in brackets

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Best answer

Very, very, late answer but i'll do it anyways.

After Bonnie obtains a Zygarde Core, with only 2 existing in the Kalos region. Team Flare finds about this, they start to stalk Ash + Crew. Serena tries out the Master class against Aria to become Kalos Queen, then fails. Ash then meets Alain, a powerful trainer who was Pro. Sycamore's former assistant, and secretly a Team Flare member who owns a Mega Charizard X. Ash then finds Diantha, who tells some more information about Team Flare. Eventually the Kalos League rolled by, and Ash's 8 badges grants him permission to challenge in it. After making it to the finals, Ash loses to Alain. Team Flare already have taken over Z2 and enough cores to make a 50% Zygarde. Team Flare captures Ash and his Pokémon. Alain then reminds himself Team Flare is not made for Justice, but for Destruction, then quits Team Flare. He rescues Ash and then they join forces to save Kalos. Z2 Zygarde destroys Lumiose City, but Ash and Z1 10% rescued the citizens of Kalos. Mairin, Steven, and Serena found Chespie, Mairin's Chespin captured in Lysandre labs. All 3 of them then rescues Chespie and finds a mysterious rock shapes like a Zygarde which then absorbs Chespie and her energy. The rock then starts to move over to Anistar city Sundial. Olimpia tells Ash that she predicted if the Zygarde and Anistar Sundial meets, the world will end. Ash and all the gym leaders fight to stop it, but it never stopped. Squishy and Z2 becomes Zygarde 100% Forme, and destroys the Zygarde-shapes-boulder and rescues Chespie. The 2 Zygarde cores tells Bonnie goodbye, and disappeared to protect Kalos. Serena puts on a show to celebrate Kalos' protection. Ash then tells everyone he has to go to the next region. (Alola.) And there goes XYZ.

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I think you forgot about ash greninja happening and the left over crazy roots appearing, and Proffesor whatshisface trying to restart team flare and brainwash clemont, but I don't mind, 'cause I saw those episodes.
3 votes

Ash fights gym leaders fails to win again

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Precise and to the point. I like it.
this gets upvoted, but it is far from BA.
there is so much complicated stuff withda team flare and the zygarde
steamcrusader, all that Team Flare and Zygarde stuff is filler now. Rapty nailed it.
What about major plot points like, Oh i dunno, Ash greninja?