Train, Release, Store in PC

Release: Honchkrow (sowwy T^T), Box: Mandibuzz, Train: Yveltal

Kecleon, Chatot, Dunsparce

release kecleon, box chatot, train dunsparce

tyrunt, copperajah, marowak

box:tyrunt, Train: copperajah, Release: marowak

Mightyena, Houndoom, Absol

Train Houndoom, store Absol, and release Mightyena.

Skuntank, Drapion, and Alolan Muk

Box: Skuntank, Train: Drapion, Release: Alolan Muk

Pachirisu, Dedenne, Morpeko

Train Morpeko, Box Pachirisu, Release Dedenne
(I could go either way with pachirisu and dedenne but its one of the few non legendary/mythicals im missing from my home dex)

EDIT: forgot damn, uh,
Mimikyu, Togedemaru, Emolga

Train Mimikyu, store Togedemaru, and release Annoying Stupid Flying Squirrel Emolga.

Luxray, Magnezone, and Electivire

Release: Luxray, Box: Magnezone, Train: Electivire

Beautifly, Butterfree, Vivillon
Funny how such a cute/pretty butterfly mon has no. 666 in the pokedex @_@

Train Vivillon, Box Butterfree, Release Beautifly

Zebstrika, Excadrill, Haxorus

Train Haxorus, Store Excadrill, Release Zebstrika

Vikavolt, Musharna, Cryogonal

Train Vikavolt, Box Musharna, Release Cryogonal

Heracross, Scizor, Pinsir

Box: Heracross, Train: Scizor, Release: Pinsir

Carbink, Shuckle, Stonjourner

Train Stonjourner, Box Shuckle, Release Carbink

Mew, Celebi, Jirachi

hmmm... Like all 3 of these... but, I guess:
Release: Mew, Box: Celebi, Train: Jirachi

Zarude, Cacturne, Shiftry

Train Cacturne, store Shiftry, and release Zarude.

Crabrawler, Stufful, and Passimian

Box: Crabrawler, Release: Stufful, Store: Passimian

Lopunny, Diggersby, Cinccino

Train Cinccino, store Lopunny, release Diggersby easily.

Tsareena
Swellow
Roserade

Train: Tsareena, Release: Swellow, Box: Roserade

Leafeon, Sylveon, Umbreon

Train Leafeon, store Sylveon, and release Umbreon.

Clefable, Wigglytuff, and Blissey

Train Clefable, Store Blissey, Release Wigglytuff

Pichu, Pikachu, Raichu