This occurs after the events of My Little Pony: Legend of the Harmonia, when Logan defeats Vexis and returns home to the Pokémon world and continues his duties as a Guardian, as well as explore around the world once more.
Its several months after saving Equestria, Logan dons a new attire and shorten his hair a bit, as well as gaining three new members of his team. He left Chika, his Meganium, with the Celadon City Gym Leader, Erika, so that she can stop battling and just take time to relax, and is fond with the Gym, so he entrusts his starter to the Gym Leader.
Abby, his Absol, decided it was best go out and explore on her own accord, to try and be more social with other Pokémon, as well as do what she does best: Scout for disaster.
Yukionna, his Frolass, was allowed to return to Sinnoh near Mt. Coronet so she can enjoy the winter time, and continue to serve as a guide to those who wish to brave the blizzard that occurs there for Trainers.
While they are no longer in his party, they are considered on Reserve and will come back to Logan should he request it, but he feels that they need time to themselves.
He offered to allow Leon and Lerita go to, but they felt they shouldn't allow their Trainer into danger without their protection, and continue to serve as his guardians till the end.
Celei knows that she was gone for seven years and feels that she shouldn't leave his side, given how lost he would be without her around. He does allow her to return to Illex Forest to make sure things are in order before returning to his side.
With that, Logan was able to 'recruit' three new members of his party to fill the void of the three he let go for the time being.
First is Miako the Ninetales. She was found near the Abundant Shrine in Unova, after Logan's visit the Shrine of the Forces of Nature, where she stopped him from leaving, as she sensed he held the power of Ninetales in him and proved it by turning into his Kitsune Forme, a shiny Ninetales with green tipped tails and spiky mane. She felt the soul of Latios in him as well, realzing he was the Eon Guardian and recalled seeing another that she was reminded of in the past, 500 years ago. This turned out to be Mason she seen, and said that he felt a similar feeling in him that she does in Logan.
Miako is an old and wise Ninetales, but can be easily angered if someone tries to mess with her tails, or piss her off in general. Aside from that, she is caring and kind, and very loyal to those she can trust, namely Mason whom she met when she was a Vulpix and sometime after becoming a Ninetales, and Logan.
She has lived for almost 625 years, has a Gentle Nature, Hidden Ability Drought, and the moves Fire Blast, Will-o-Wisp, Dark Pulse, and Psyshock. She also has the special ability of cursing others, the curse transforming individuals that try to grasp her tails, into a Pokémon randomly.
Being a Kitsune, she also can turn into a human and back into a Ninetales at will, as a means of disguise and blending with other people. (Picture TBM)
Second is Sarisia the Aegislash. She was discovered during Logan's visit over Kalos. He discovered an old ruin in the outskirts of Lumiose City and explored it and came across the old Aegislash, who said she was once a knight for the ruler of the ruins 320 years ago, and was devoted to keep her King, and allies, safe from harm as she was one of the holy paladins of Arceus.
She died after an ambush was set up to assassinate the king and she fought with her last breath, protecting him and her allies. Because of her actions as a Paladin, Arceus gave her another chance and had her soul reborn in a sword, becoming a Honedge. She has been guarding the ruins ever since, having evolved 400 years prior.
She senses how Logan is as a leader, and would think he would be a king in the future, but he doubts that as he just rather explore the world and other dimensions outside this one. She then vowed that she would serve him as his sword and shield, literally.
Sarisia has an Adamant nature, and the moves Sacred Sword, King's Shield, Swords Dance, and Shadow Sneak.
Logan is capable of wielding her as secondary sword, while she has her shield around his right arm, acting as a bracer, while he wields his own weapon.
His third Pokémon is Levian the Kingdra. This was formerly one of Clair's Kingdra, when Logan came home to visit, she asked if he could help her out and take on of her Kingdra's to train, as well as see the outside world, having been living in the Dragon's Den for a long time. He agrees, thinking it be good to have at least one reminder of home, seeing he never visits Blackthorn as much as he wants to.
Levian has a Hasty nature, and knows the moves Dragon's Dance, Draco Meteor, Hydro Pump, and Surf.