First time the fact of the alien options inside the omnitrix aren't just a DNA skin-like suit Ben changes into, but actually unique entities with their own thoughts, memories, and abilities, evidenced by Grey Matter saying "this is Grey Matter talking, not Ben!", after telling Grandpa & Gwen different alien tech to grab.
First appearance of "The Organization."
Throughout this show, there are Stargate SG-1 (1997) sound effects and weapons. For example, when the Organization activates the device, the sound effect is of the Stargate opening sounds. The weapon the Organization use is clearly an Ori Staff weapon.