Powers and Trigger's initial appearance is in Scaryoke. They show up and point out to everyone that the government knows something about the portal and the conspiracies happening in Gravity Falls. Here are a few things we can learn from or about them.
30 years ago they investigated some strange readings in Gravity Falls. My belief is that they were looking into the portal. I say the portal was opened on July 4th, but by the time they got there, everything was normal. This may be where Stan learned to distrust the government. Now, the agents may have learned a few things nonetheless. Remember, Powers had some idea of a conspiracy connected to the town.
Powers and Trigger, like Blendin Blandin in season 1, are an "Easter egg" in several episodes this season. They have cameos in Sock Opera (at Mabel's play), Soos and the Real Girl (at the mall), Little Gift Shop of Horrors (in Hands Off, at the bowling alley), Society of the Blind Eye (behind Soos' car when Wendy throws the disc out the window), and The Love God (at Woodstock). Oddly enough, though, they do not appear in Blendin's Game, leading me to believe that it was originally scheduled for later in the season.
There is also an Easter egg in Sock Opera where there is a listening device hidden in the Mystery Shack floorboards, with the eagle eye symbol on it. This shows why the camera pans down slowly from Dipper and Mabel's room at the end of Gideon Rises. There is noticeably no listening device there, only a pipe that says "Bill is watching" in code.
Obviously, the agents make their second official appearance in Northwest Mansion Mystery. You may have also noticed that they were there when we were introduced to the other party guests. As of this writing, Not What He Seems is not out yet. Just be sure that we will find out a lot more about these guys in that episode.
The agents are alluded to in one, or possibly two, cryptograms. The first is in Sock Opera: "We've all had some fun tonight, but let's not forget who the real 'puppet masters' are: reptoids who have infiltrated our government." Reptoids are reptile-like aliens. I believe it means that Powers and Trigger are aliens. We did get a joke about aliens playing a part in season 2.
The other cryptogram is "At the play or at the fair, I always see them standing there. Dressed in black they're on my lawn, but when I turn my head they're gone." This one is the end card from The Love God.
