Within paragraphs of the book's end, we see that Nikki's life is back on track in the mortal world. She tells us:
I wasn't going anywhere. The Tunnels had forgotten about me. Jack's sacrifice meant that I had my family back, and even though our fractured relationships had a ways to go, my home life was suddenly a stronghold in my otherwise messed-up world. (33.53)
So that's a relief. In the beginning of the book, Nikki knows that she has six months until the Tunnels claim her for eternity. This kind of puts a damper on her ability to reconnect with her family, you know? But now she's able to do that… but it's at the cost of her relationship with Jack, since he took her place in the Tunnels.
More importantly, however, Nikki's internal circumstances have changed, too. She became a Forfeit in the first place because she couldn't handle all the pain in her life and needed it gone. But as she reflects at the end: "The pain of loss was fresh every night, but I no longer begged to have it taken away. I owned it" (33.54). So that's a major change for Nikki. She's no longer running from the harder parts of her life, and instead is ready to claim them as her own.
Nikki resolves to find a way to get Jack back from the Tunnels, but in the meantime, he visits her in her dreams each night. She suspects that this helps him retain some sense of himself, so that his entire life energy isn't drained away. The last few lines of the book reflect this:
We discovered long ago that we can't touch, even in our dreams. I am as much of a ghost to him as he is to me. We are a breath away—and a world apart—from each other. He doesn't know where he goes when he's not with me. He doesn't think he exists anymore, except for in my dreams. I think he is right. And I tell him to hang on. I will never stop dreaming of him. I will find him. (33.58-61)
Wow. That's some pretty emotionally charged stuff. We see from this ending that Nikki is totally devoted to Jack, and knows that he's devoted to her, too (unlike in the start of the book, when everything about their relationship was up in the air). We also see that Nikki is totally resolved to find him, which echoes how committed Jack was to finding her when she disappeared, which she only learned about midway through the book when they opened up to each other again.
So in a lot of ways, the ending resolves a bunch of tensions between Jack and Nikki, even though they can't physically be together. This is actually totally appropriate, because it was all the emotional angst between Jack and Nikki that sent her spiraling into the Everneath in the first place. So working this stuff out shows how much they've overcome. Yay.