This run is extremely bad, but it serves as a first submission and a showcase of the route I've been working on (that I barely remember during this...)

There are many things I haven't figured out yet like when to get what upgrades, when to switch them around, the exact paths to take and all that. I also don't know if interacting with the other ship after beating the final boss is obligatory to triggering the end cutscene. A lot is left to do here, but maybe this could serve as a good starting point.

I've also found lots of skips not applicable in any% but would be useful in other categories.