You were pretty near the end, (mostly just Massive Martia), which is I hope a fairly fun boss fight - if you do download the exe version, here are some values you can change in the settings ini which allow you teleport round set areas of the map, so to get back to the room before her and play the final boss.
Download and extract files:
Open Settings.ini in Assets folder
change
allowshortcuts=0
to
allowshortcuts=1
save Settings.Ini
start game and press play
Press T 7 times (till you teleport into a room with all the powerups) collect the powerups you want
Press T 4 times (till you teleport to a green room with 2 lasers and 2 red flying drones)
go left and fight the boss...