For anyone who's confused, so am I but I think I have the hang of it.
5 years have passed since the last episode of Season 1 so probably in the year 2015 or 2016 and everyone are full fledged adults. Most of the Team (Superboy, Robin (Who is now Nightwing), Miss Martian, Rocket, & Zatanna) are all league members and now mentoring the new generation of Young Justice (Wonder Girl, Blue Beetle, Lagoon Boy, etc). Miss Martian and Superboy have broken up and she is now dating Lagoon Boy and they're now setting up the show for an alien invasion. Though the whereabouts of Kid Flash, Artemis, Aqualad, Red Arrow and Speedy are still yet to be revealed.