The following article contains spoilers from Dark Crisis: Young Justice #1, on sale now from DC Comics.
With the Justice League presumed dead and the surviving heroes left in mourning, it seems that no one has their eyes on Pariah and what he may do next. However, Dark Crisis: Young Justice #1 (by Meghan Fitzmartin, Laura Braga, Luis Guerrero, and Pat Brosseau) may have exposed the villain's next move. The disappearance of Young Justice hasn't been noticed by the other heroes yet, but where Robin, Superboy, and Impulse ended up highly resembles the same kind of prison Barry Allen experienced at the hands of the cosmic antagonist.
The boys have been seemingly sent back in time to periods of their lives when they were happier as members of Young Justice. There are even built in distractions, possibly meant to ensure that they don't look too closely into where they've been sent. All of this mimics Pariah's usual method of entrapment, suggesting that he may be behind it all.
At first glance, Pariah appears to be the obvious suspect. Aside from the fact that the boys are trapped in a world tailored to their desires, the cosmic villain appears to be one of few people capable of doing such a thing. The issue showed that they weren't far from Superman, who would have noticed if they were forcibly extracted. The only conclusion is that it happened so fast and silently that not even a kryptonian could catch it, suggesting a massive amount of power was in play.
The prison itself is insidious, feeding the team's secret desires. In this case, they have returned to a time when things were simpler. While Barry Allen was instantly seduced by his prison's allure, the three younger heroes immediately recognized that something was wrong and they were all misplaced.
Although the trio quickly recognized that they were in the past, a "threat" came to their attention, distracting them from investigating. The three of them know that they're not supposed to be here, but the illusion is so real that they can't intentionally ignore a threat without someone possibly being hurt.
All of this seems to support the idea that Pariah is behind this. Crafting a prison they would never want to leave, or never could without their guilt destroying them is easily within his abilities. The only questions that remains is why he has chosen to do this to Young Justice instead of one of the many other heroes who could impede his plans for the impending Dark Crisis.