I think the deal Hopper made with the DoE wasn't just "Give us access to the gate AND keep everyone safe and we'll give you Eleven" He said, "You'll give us anything we want."
Hopper is a smart enough, and jaded enough, man to realize that when you've got the Government by the balls you go all in, and him being picked up right after the events by the DoE agents and him knowing about Eleven still being alive in the Upside Down only further shows he's now on the inside. But why is he on the inside? What does he have to gain and what would the DoE want with him if they didn't have to keep him around for something?
The fact is, they both still have something enormous to gain. Even bigger than what has happened so far.
This is where the Stephen King mythos comes in especially heavy. The first thing I thought of when they showed Eleven in the sensory chamber trying to spy on the Russians was "Hold up. this is Todash space. She's in Stephen King's Todash space."
Now, for those of you who don't read King heavily, Todash space is described by King as "A space between spaces, the cracks of all the universes, only the most vile and evil creatures exist here, and they don't truly live, they simply exist. To get here you have to be a powerful psychic/have access to insane technology, or be cursed by fate." For a famous comparison, Pennywise the Clown from IT lived in/existed in Todash space... and was one of the weaker creatures here. And furthermore, to get into Todash space you often times run into something he called a "thinny" or a weak spot in reality where the universes have eroded thin. A common side effect of thinnies (which can be hundreds of miles in size or the size of a dime) is a strange mist or weather phenomenon, similar to how all of the Upside Down is. The reason the creature never entered our world before was because creatures born in those spaces can't get out unless they get extremely powerful from devouring each other or from being contacted by people/things from other realities. Eleven touching it effectively "honed in" on our universe's frequency allowing it to start coming in and out.
I believe the King influences here are hinted at strongly because of the near perfect descriptions of Todash spaces and the fact of all the influences this story has, NONE are as out right obvious as all of the Stephen King ones. The show typing/lettering is exactly how his classic novels were done (the big bold red letters). The first episode Will is asked "You're not even scared of... clowns?" a direct reference to pennywise (just before he is abducted by a todash monster effectively.) The bullies call them "Those Losers", a pretty obvious reference to the Losers Club from IT as well, and the knife scene where the bully has Mike jump off a cliff is from IT also. But on top of that King not only gets called out by name when meeting Eleven's mother, but the security guard is reading a novel with Stephen King's picture on the back whenever Hopper breaks into the Morgue to check out the fake body.
Now, what does this have to do with the DoE and Hopper? Well, it goes back to exactly what the Upside Down is. It's not a different universe. It's simply the other side of our own reality. It's not a different tightrope, its just the side that doesn't get sunlight.
It's the space between two spaces.
The fact that Eleven, as a prebuscent child without a fully developed brain, is able to get here already shows that once she gets more used to her powers (or finds a way to tap into them with more emotion, as she did when she turned 10 people's brains to mush at once) she will only get stronger. So, if she's only in the underbelly of our universe already what else could she do?
Entire other realities. Universes where the Cold War DID happen. Universes where Alexander the Great didn't die young and actually conquered all of the known world. Universes where Coca Cola never existed. Universes that are thousands of years further advanced in science and medicine, where a little girl isn't at risk of dying from a disease of any kind.
Hopper told them he wants to use Eleven to find an alternate universe where his daughter is still alive. And he said he would work with them, now in the stead of her evil "papa," to help her tap into her potential which was clearly raised once she developed feelings for Mike and his friends. And she is in the Upside Down now, not because she can't get out, but because she is staying there to both:
1. Prevent more creatures from coming through and develop her powers
2. work on opening holes there to other universes (because the stability of that part of our universe is clearly weaker than the normal one because the creature is able to break through easily, as are normal humans if they're fast enough.)
I think the season will start with her opening a hole to an entirely alternate universe (or finding more of the monsters/different monsters in the Upside Down) and it will cause ripples in the Upside Down and our own universe. Will is going to be the villain in the normal side for the most of the story, maybe even being fully possessed by an entity far smarter and more evil than the monster we saw, because never before has one of these creatures tried to cause gestation in humans, and it's only logical to think that a child of a human/monster hybrid will be smarter, or it could just outright be a more evil and sentient parasite that simply spawns more children and hides in the shadows and was even using the monster in the same way to find more hosts. I'm much more inclined to think the main bad creature wasn't the thing Eleven killed, but a Parasite/doppleganger as well because of the enormous implications this would cause (their friendship/circle being challenged enormously next season is a great way to go) and because the science teacher was watching The Thing whenever they called about how to build a sensory deprivation tank. You could pick ANY sci fi movie/horror movie to show there, but why the Thing? Because it, just like many of Steven King's Todash monsters, can turn into anything they want or take control of bodies out right after assimilating them.
I think Will gets solved by episode 7/8 and that's when we find out the real threat is still the new reality, and it gets solved/delayed in order to set us up for season 3, with a nearly mad to see his daughter Hopper either going into the universe himself or stealing her from the other causing who knows what kind of temporal disturbances