This is what I used to beat Atropos:
Blue Hull rank 5
Bomb Mod: Leech
Ship Mod: Shield and Defensive Laser
All weapons are Bullets with Split, half with Acid and half with Affliction.
This might not be the best way but this is what I used.
Scientist: Sir, we've finished creating a model of high-tech armor to help exterminators fight the Glooples.
Foreman: Excellent... now, make it self destruct after a single hit.
Bandit Soldier: Sir, a magician wielding magic of one of the greatest wizards in history has been spotted heading straight for the base! What are your orders?
Bandit Leader: Hmm, this could be bad. Send one swordsman, one archer, and one mage to fight him one at a time. If that fails then I will attempt to kill him all by myself!
Nice game, but I personally think the game this is based on, Warning Forever, is better. The movement control in this feels stiff, and the gun aiming in Warning Forever is certainly better than this game. But the upgrades and achievements are great additions.