Oh, and because this didn't fit in the original comment:
This game has a sequel, just not on kongregate. It's multiplayer and everything. I believe its plazmaburst.net.
Beat the entire game on hard without getting any armor upgrades. Here are some tips.
1. If you never see an enemy, they'll never see you. Some levels start with enemies to the right of you, look to the left and back up into them to see what I mean.
2. If an enemy shoots another enemy, they'll fight each other to the death.
3. Plasma cannon fully upgraded kills pretty much everything in the game in one shot.
4. Hold down left mouse button, tap 5 and 6 as fast as possible, aim away from face, enjoy. Better to let what this does be a surprise.
5. Memorize enemy spawn points so you can take advantage of the sight trick.
6. Once an enemy does spot you, they'll run themselves right out of cover most of the time.
7. Grenades suck against robots, red aliens aren't robots, due to their unarmored legs, they die in one hit from grenades.
8. Your ally makes a good shield late game.
9. If you see an empty, flat hallway, shoot down it. It's always a trap.
If you go to fishport, you should see a red mage there next to the enchanter. Talk to him to get your instructions, after you do everything, you get easily bar none the best weapon in the game. (I could solo everything with it.)
The only mistake you made is that A ninja could sneak up Right behind a pirate and stab them in the back. Besides ninjas are fast enough to confuse pirates and there guns take like 5 seconds to reload
 "Plazma Burst: Forward to the past"){kind=icon}
 "Feudalism III"){kind=icon}
 "Pirate Vs Ninja"){kind=icon}