Only level 5 nuclear grenades damage Dr. Mordae! With the grenade launcher equipped, check the meter right under the ammo counter at the top left. Make sure it's on lv. 5. Press ] by default to increase the tech level. More info + easy boss guide below if anyone's interested.

You can find scanner(radar) and other weapon tech upgrades throughout the game, mostly in secrets, but the only one you're forced to find as an objective is the "Lv. 5 Implosion Tech Module" for the grenade launcher -- I think in level 8, in one of the lab rooms. You're explicitly told you need the upgraded implosion grenades for the boss too. I just forgot the ] key myself and assumed the upgrades automatically applied. So I get to the boss just using base-level everything.... Only to waste an hour running around and reloading the last level, thinking my game was bugged because the lv 1 nuke grenades had no effect. Don't be like me.

Easy boss guide: Listen to Mordae's opening speech, then the instant you get control quickly strafe and back up as he throws an exploding skull at you. I recommend just keep using the pistol on the skulls. It's good to save here if that first skull didn't tank your health, otherwise if you die or restart you'll have to sit through the speech again. Equip the nuclear grenade launcher, make sure it's on level 5, and fire ONE grenade as close to Mordae as possible and GET BACK until it explodes. They have a huge damage radius many times larger than rockets -- just stay within sight of him. Keep the pistol out while you wait for the grenade to blow up; strafing to avoid fireballs and shooting any skulls he throws. Mordae walks around, but he usually keeps within range of the grenade til it goes off as long as you stay within sight. You'll know if it hit, because Mordai will teleport away. After a couple seconds he reappears somewhere else (check the scanner if you can't find him).

Just repeat the above process of firing a grenade close to him, then backing up and using the pistol on the skulls and avoiding the fireballs. After 3 to 5 grenades he's dead. It's really a quick and easy fight, just remember only level 5 grenades work. Also, only use one grenade at a time: launching several at once just wastes ammo because he teleports after the first one blows up anyway.

If you need more grenade ammo there's a few rounds scattered in the corners of the arena. There's also two secret walls with 100-health packs in each, but I only found them by accident so don't ask me where.