What I assume is the final boss is definitely no joke. I'm pretty sure I will have to go back to a previous save because the computer is throwing more enemies at me than I can keep up with. Fortunately it seems like they spawn from predictable locations, so if I position my soldiers correctly then I will be more successful.
For my next run I need to be more careful with how I spend my resources. This time I didn't spend much thought into the build order of facilities or how I prioritized research.