The Time Skip was an event which covered the four years in which the Elements of Dischord fled Equestria to improve their ranks. During the Time Skip, several important things happened in the lives of each character (such as Atticus being discharged from the Town Guard) leading to a lot of "off-camera" character development
The Time Skip was explained in the RP by a group of ponies from Aperture Science installing a relatively stable AI (yet another Portal crossover) into the Ponyville Town Hall. The AI (Wheatley) almost immediately announced that it was about to conduct a "test" by using modified portals to send a select few ponies through time. The "test subjects" regained consciousness with the bodies and memories of their future selves.