Trying to find the details of a particular story I read it online in maybe the early 2000's or even late 90's. Not sure if it was ever physically published or just online. May have been published periodically or as several short stories? I've looked for it a few times but never turned anything up.
If I recall correctly, the story spans from the near future (2030-ish?) to the distant future (~100,000's years AD). With each chapter/instalment the narrative jumps forward, sometimes years then later 10,000's of years at a time.
It's written from a first person perspective but, I think later it gets a bit more complicated because there are multiple copies of the consciousness separated by great distance, so things like relativity and time dilation are dealt with.
It story starts with a test flight pilot (Air Force?) "waking up" inside a simulation. they're told there was an accident and they "died" but scientists were able to extract their consciousness and boot it up. There's a process of tweaking the software so everything works but, over time, the character becomes an increasingly capable simulated pilot, flying various aircraft. Over several chapters we see the pilot flying aircraft, then spacecraft for humanity and becoming increasingly less human as their programming is edited and tweaked for purpose.
Later in the story, when piloting vast interstellar crafts, the protagonist meets a group of alien AI in the form of robots. Unlike the protagonist, these beings have a limited memory capacity, causing them each to "die" after something like 200-300 years, after which their hardware is reset and begins anew. Earlier in history of this group, they were responsible for wiping out the species that created them, though they now regret it.
I believe that's more or less where the story ends. Possibly with this alien robot race caring for the remnants of humanity or something. I think there's also reference to other AI races and that AI is the dominant form of life in the universe, with biological life and biologically-derived intelligence (like the protagonist) being quite rare.
Generally, I remember being struck by the massive scale of the story, in terms of time and space, the logistical challenges of communicating over vast distance and the psychological and cultural effects caused by different perspectives of time.
Does that ring any bells to anyone?