Dark Matter season 1 ended with Jason Dessen (Joel Edgerton) getting his family back and fleeing into the multiverse to find a new world to settle down in. This ending was lifted directly from the book, which has allowed season 2 to provide an authentic continuation of events from the source material.
Considering the high-concept drama the Dessens endured in the original 2016 sci-fi novel, the ending they got was probably the best they could have hoped for.
That being said, author Blake Crouch heavily teased an alternate ending for his main character that ultimately fell apart. I've always thought it would have been an equally great way to end Jason's arc, if not even better. Thankfully, Crouch has capitalized on his transition into Dark Matter showrunning duties to make it happen. Furthermore, the alternate ending isn't just canon in the live-action adaptation; there's also nothing to stop it from being part of the official book lore either.
FULL SPOILERS below for Dark Matter season 2, episode 8, "The Basic Oneness of Everything."

Dark Matter just gave Jason the happy ending with Amanda that the book teased
Dark Matter season 1, and its source material, is built around Jason and Amanda's (Alice Braga) tumultuous journey through the multiverse. Amanda's presence in the Box is due to her burning bridges in her original universe, and Jason is trying to get back to his wife, Daniela (Jennifer Connelly), and his son, Charlie (Oakes Fegley). Along the way, it becomes clear that the shared trauma and emotionally draining experience have resulted in Jason and Amanda developing romantic feelings for each other.
However, Jason commits to the near-impossible task of getting home to his original reality. Heartbroken, Amanda protects herself by parting ways with Jason to start a new life that isn't defined by traveling endlessly in the Box. If things had gone even slightly differently, such as Jason feeling particularly run-down that day or exhausted from their journey through the multiverse, I can certainly see him caving to his feelings for Amanda and leaving his old life behind.
Season 2, episode 8, "The Basic Oneness of Everything," returns to that very decision. With a new version of Amanda bedbound with a dicey injury that could go either way, an equally new Jason is forced to delay their return to the Box for weeks on end while she recovers. Although he tries to justify his decision not to abandon her with all sorts of moral window dressing, it's obvious the core reason is that he's fallen in love with her.
After Amanda recovers and opts not to go back into the Box with Jason, Edgerton's character then makes a few more last-ditch efforts to find his universe. He fails, and I'm convinced it's because his subconscious is clinging to the idea of being with Amanda rather than risking being stranded in some random reality without her. By the end of the episode, they're officially an item and implied to be shacked up together, away from Laurel's (Margo Martindale) waystation. So, it seems Dark Matter's "main" Jason and Amanda could have been equally happy if Jason had let go of his old life.

I'm choosing to believe that Jamanda is also Dark Matter book canon
By design, Jason spends most of the Dark Matter book with Amanda rather than Daniela. As a result, it's easier to pair them off as a couple, even though Blake Crouch never actually made them get together. Meanwhile, hearing Jason always talking about how great his wife is starts to get a little grating. The show fixed that by doing a better job of showing how well-matched they are, but still, I was always more drawn to the idea of Jason and Amanda as a romantic pairing instead.
I'm sure that was probably Crouch's intention. Thankfully, he's sort of retroactively made that the case with "The Basic Oneness of Everything." The twist that rounds off the book, which reveals that Jason (and Amanda) have been duplicated while traveling in the Box, is explored even further via the new flashback sequences set in the wake of a version of Amanda being injured. Considering this widespread doppelganger phenomenon is also book lore, I think it's safe to assume these scenes with Laurel also happened off-page in the source material.
Note: I also think it's pretty clear that Laurel's speech about life and change is the catalyst for helping Jason move on with Amanda. That's why it's never happened before now.
In other words, I think there was always a version of Jason and Amanda out there in the multiverse who settled down in Laurel's world. It's just taken until season 2 for us to see it play out. The reunion between this Jason and his original son, Charlie, toward the end of the episode was also a masterclass in tying up loose ends. Choosing Amanda over his wife was Jason's way of letting go of his Daniela, but letting go of his son required some face-to-face time for one last goodbye. It was almost too emotional to bear, but I'm glad Dark Matter made it happen.
Dark Matter season 2 is streaming now on Apple TV.
