Alright, here is my way of incorporating him into the SSE:
Yoshi, Link, and Pikachu have all assembled a rebelion team at this point. They're makignt their way through many obstacles in an attempt to reach "The Stadium. Along the way, they pass by a Pokemon crazed metropolis. However, Cipher (from Pokemon Colosseum and XD), have corrupted the city...
See, the Cipher organization had their plans to convert all Pokemon into Shadow Pokemon foiled. So, they made a deal with SSE to provide them with creatures from the Subspace Army to spread around. Cipher Admins were tasked to do this. Their plans were voided once again, this time by the Pokemon Trainer (from Brawl).
Now, Mirror B. (if he's in so is his theme, so...) has been distributing Subspace creatures to Trainers in the from of Subspace Balls (they look like Pokeballs). He's been doing this by going to cities which are obsessed with Pokemon and entering tournaments to demonstrate their power. He was entering a tournament in that city when he saw Yoshi, Pikachu and Link strolling by. He was instructed by Cipher leader Evice, that if they defeated that group, the SSE would grant them a large reward as they had foiled an other invasion by the SSE.
Mirror B. Challenges the group, and selects Pikachu as a foe (naturally as he is a Pokemon). The battle takes place at the town's enormous Colosseum. Pikachu is expecting a 1-1 with another Pokemon, but is mistaken. Mirror B. uses two Pokemon at a time, and they aren't even Pokemon. Pikachu is getting beat up, but just in the nick of time, guess who shows up...
Pokemon Trainer was going town-to-town defeating Cipher's admins, snagging their creatures, using purification methods, and converting them into Pokemon. He was passing by the last town he needed to purify, and he ran towards the Stadium. There he saw that Mirror B. was beating a Pikachu with a lop-sided team (Yoshi and Link are now captive).
Pokemon Trainer jumps from the grand-stands, throws a Pokeball, Squirlte jums out, and aides Pikachu. The duo defeat the admin and demonstarte how regular Pokemon are superior to corrupted creatures, and move on.