Apart from the eight weapons with visible slots and the eight "hybrid" weapons that can be created with the Crack skill, there are 3 bonus weapons that can be found in the game. The Massacre, which uses your Health for ammo and blows up enemies real good, is gained before the final boss battle if you went the pacifist route; the Banana Gun, which shoots explosive bananas (notable for being subject to gravity), is found in a weapons cache that can be found via abuse of the MPFB Devastator; and the Null Driver, which we won't spoil for you here, is found in a well-hidden Bonus Level and is locked away unless you've gotten all of the other secrets.
You can change a major plot point by planting the Trapmine you find in Sector 8 on the teleporter by the exit of said level.
The staticky noises in Asha's theme song, as confirmed by Remar in his speedrun videos, are actually distorted clips of the composer saying evacuation notices and babbling about beer. Once you know what the words are, you can hear it pretty clearly if you listen.
The room where Iji fights Assassin Asha for the second time is modeled after the Ridley battle room in Super Metroid. Only with electricity in place of lava.
If you stay long enough outside on the sectors where you can see both Tasen and Komato spaceships in the background, you can see that after a while they actually shoot each other down.
The term "Ultimortal", used as the name for the final and hardest difficulty, is an in-joke between Daniel and his friends, and is also his usual username on different websites
One of the bosses was made into a robot instead of being piloted by Komato as originally intended because of its attack pattern.
Ansakie and the common assassins were made female to differentiate from Asha, otherwise some players would end up thinking that Asha was being ridiculously persistent when they faced the common assassins.
There are ten main sectors in the game, with the last one being labeled "Sector X". The Roman numeral for ten is "X".
If you fully upgrade any skill, its number is also replaced with "X".
As revealed in the official game guide, triggering the dialogue in Sector 2 where Dan claims Iji isn't strong enough to take on the Elites will make Iji's sound effects the angrier aggressive run versions, even if you're a pacifist - but if you cancel the conversation before she gets angry, it will remain normal.
There are persistent rumours based on in-game hints that beating Hero 3D 242 times would unlock something, and allegedly some players attempted it. The manual revealed it was just a Red Herring.
Remar has been saying since version 1.3 that he would not release any more updates except to fix major bugs. We're now up to version 1.6, which has added minor subplots. He also said that it's more that he doesn't expect to be up to making a new version, but something draws him back.