Is this really a Scratch game? This is probably the best one I've played on this site so far! Congratulations on making a surprisingly fun game!
I decided to play with all three extra difficulty settings on, which probably made the game more enjoyable. I chose to keep the axe in my first run, but I kept getting lots of upgrades for bullets. It wasn't clear if they would benefit the axe's projectile, so I chose to ignore them.
I got to the Venomite battle on my second run, but I ran out of time to finish the fight before the next wave started automatically, which made Venomite's health bar and the boss music go away. I feel like more time should be given to finish the boss waves with the Enemy Territory setting active, as I got run over by the mobs that spawned in while the boss's patterns were still going on.