In this episode, we learn some secrets about Yves, and according to Frank Spotnitz, this is where we start to see the Gunmen's mythology open up.
Morris Fletcher is apparently snatched by aliens (apparently the Gunmen in disguise!), and Fox Mulder runs into Jimmy Bond. I've heard rumors that this episode may also feature a second appearance by Skinner, but I haven't seen any concrete evidence for it.
When Ash and friends hear of a virtually undefeatable trainer operating nearby, they seek her out, only to see first Brock's Vulpix and then Ash's Cyndaquil take heavy abuse from her Skarmory-despite its disadvantage against the Fire element.
Magneto reveals the his plans for the winners of his challenge - to fully unlock their powers with a machine he has built. Back at the mansion, those left behind regroup, and decide to pay Magneto a little visit.