Although we spend the entirety of Dark Matter within the city of Chicago, the novel's setting isn't as straightforward as it may seem. That's because we visit the Second City in several different parallel universes, each vastly different from the last.
Two Sides of the Same Coin
First, there's Jason's home universe. This universe is defined by Jason's home, a quaint brownstone dominated by the organized chaos of family life. This is "a place of safety and comfort, where [Jason is] surrounded by family," which is why he's so upset when he visits other universes and finds his house looking wildly different (3.42). In scientific terms, Jason's home is the "constant" that he compares against the versions of it found in other universes.
The first of those universes is Chicago2, home of Jason2. This setting reflects Jason2's choice of science over family. First, there's Velocity Laboratories, which is so advanced that it seems like it was plucked out of the future; you're not going to find it in "real" Chicago. But more importantly, there's Jason's home itself. Instead of having that great lived-in feel, Jason2's abode is fancy yet sterile, a reflection of the material boons that came at the expense of his personal life.
Infinite Sides of Infinite Coins
And that's one of the normal Chicagos. After escaping Jason2's world, real Jason explores a series of insane alternate universes. There's a version of Chicago that's a frozen tundra. There's a version that's been decimated by a creepy plague. There's even a version that's straight out of Star Trek. On these one hand, these disparate settings are merely a reflection of the emotional turmoil Jason is experiencing. On the other hand, though, they give us a sense of just how infinite the universe is.
Even freakier than these universes, though, are the ones that are almost like Jason's home, the ones that seem just about real, but aren't quite. Jason explains this freakiness by turning to the theory of uncanny valley, which is that "when something looks almost like a human being [...] it creates revulsion in the observer" (11.2-3). Like, a really, really realistic android is scarier than a plan-old robot, because the realistic one starts actually messing with our perception of reality.
In a similar way, Jason is simultaneously intrigued and disgusted by these almost-universes, as they heighten the feeling of homesickness that threatens to overwhelm him.