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I am in the very early stages of brainstorming for a story, and I have come up with a concept that interests me quite a bit. The only problem is that there is a hole that I can't find a proper explanation to fill. The idea is thus, a lone astronaut wakes up upon his small ship after being under the sleep of cyogenics for an innumerable number of years, centuries, or millennia even and finds himself in a universe he does not know (humanity is gone perhaps? Somehow transported to another dimension?). Coming to this discovery, he goes about progressing through the story (where ever that may take him). My main issue is, why was he put to sleep for so long? I haven't been able to find a reasonable explanation for such a question that satisfies me, an answer that makes a semblance of logical sense.

Alright, if by any chance you're trying to make this realistic, then here are some pointers. They'll probably help you think.

a) This will have to take place in the far future, as in the astronaut will have to have lived in the far future, because existing technology can't get us safely to Mars (a three month trip), much less anything over a few years in space

b) Humans are not adapted to space. We lose bone mass and muscle rapidly (they recently did a one year trial with twin astronauts), and eyesight also suffers. Our entire body is extremely well optimized for earth, and not at all for space (like putting a dolphin on a volleyball team). Arguably, legs are entirely useless in space, you can propel yourself well enough by your arms. Any setting where humans are alive in space for long will lead us to the next point

c) In a far future, with the technology to pull this off, 'humans' will not look like the humans we are today. Depending on how the coin flips, we might either be intentionally designed creatures (including 'versions' suited for underwater and space habitation), we might be full cyborgs (if you believe a person is the sum of their volition and consequences), or we might be the humans we see today, but with overwhelming life support (highly unlikely in the extreme, only if a human glorifying cult with overwhelming resources comes to power would this be possible). For more ideas, check out the affinity trees in Civilization: Beyond Earth (post the Rising Tide expansion pack), they put in a lot of interesting thought into this premise. The game itself is passable, but no Civ V complete.

d) Cryogenics, atleast the modern version of it that we're running) is probably a terrible failure waiting to be revealed, given the methods of processing of cadavers, and how new research is suggesting that 'knowledge' is stored across the body, not just in the brain. So, you'll have to have Cryogenics + Bionics 2.0 to pull off 'wakes up in space' as a premise, if you stay with normal bodies.

e) Read this graphic novel adaptation of Asimov's excellent The Last Question, should give you ideas. Other recommended media - Seveneves, Gravity, Asimov's Foundation series (kinda stretching it, but an exceptional read no matter the reason)

I would like to emphasis that this is simply a way for me to overcome a bit of a thinking block and stimulate some more interesting thoughts, I am not asking for someone to give me a step by step explanation on how to write my story. Now on to Stryker, I am thinking of having it take place in a nearer future with slightly more advance technology that we have today, I want to stick with a fairly primitive humanity. Explaining cryogenics will be an interesting obstacle, but I want to maintain that since that humanity is still on the cusp of space travel. Perhaps having it has a early version still relatively untested and something happened to caused him to be forgotten in his near frozen state.

Sounds similar to the video game “Out There.”

Einstein's relativity is an incredibly cool and incredibly perplexing thing to learn about, its so weird that something so seemingly impossible is possible. I'll keep that in mind, I just learned the math behind it in physics. 

The concept of the story is for this astronaut to wake up in a familiar, but oddly different galaxy than before. I want to keep a since of realism to carry with the idea that this galaxy he finds himself in is definitely our, but no other humans will be present. It will then move on to surviving alone and exploring what happened in his absence, perhaps with some undertones of horror.

I just want to confirm one thing. Is your story SciFi or SciFantasy? If it's SciFantasy you don't need to explain anything. In fact, even if it was SciFi you don't necessarily need to explain where your astronaut came from depending on what you want to focus on. If your focus is on surviving alone, is it really necessary to answer that question?