These are my raw notes and can do with some improvement, but the bulk of the info is there already.

This upgrade route has potential to hit sub 50m so there are a lot of potential resets going into this. My current Any% PB is 40s away from sub 50m and there's at least 40s of mistakes, so there's definitely room for improvement.

[section=Version 1.0]1.1 can be used for IL runs and most of the tricks used in 1.0 are possible in 1.1, however 1.0 is currently believed to be faster for full game runs because 1.1 has about 5 seconds of slowdown after each boss kill. To unpatch Nefarious to 1.0 follow this guide: https://www.speedrun.com/nefarious/thread/jb0ug

[section=Controls] You can use keyboard/mouse or controller, there's no reason for one to be faster than the other and you can switch between both at any time. I personally use keyboard/mouse with some controller input.

[section=Upgrades] This route buys the Charge Punch, Explosive Punch, Gyroc Missiles and the two cheapest ammo upgrades, altogether this costs 7000L. Since collecting Lucre and buying upgrades costs time it is possible that a Buster Run (no upgrades at all) is still fastest, but it remains to be seen if a Buster Run can make up the time lost to the missiles in Adept Co. Labs, Winterdown and Bramble Flats.

[section=Route]

1. Macro City

• Time starts when you close the first text box ("Yeah, I'm the bad guy.")
• Ignore all chests in this level. Complete this level as normal

2. Insektia

• Grab chests on the main route, ignore chests behind hidden walls until you grab Apoidea
• Immediately after Apoidea, break the wall and grab the coins
• Immediately at the end of the moving platform after Apoidea break the wall and grab the chest
• Ignore any other chests and finish the level

3. Sukochi

• Grab chests along main route
• Use grenade-jump-chains to skip the Trials of Man (props to Tyrant Chimera for this!)
• Immediately after grabbing Malachite (running left) head up and grab the chest, then go down and grab the next chest, then when you reach the moving spike balls (running right) head as far up as you can and grab the chest in the top corner of this room
• Reset if you don't have 7000L immediately before the boss fight
• Fallon is the healer, so use Orbital Cannon on Fallon twice and pray for good RNG that you get the quick kill
• Only use Grenade Launcher when you're sure it will kill at least one target.

4. Winterdown

• Buy Charge Punch, Explosive Punch, Gyroc Missiles and the two cheapest ammo upgrades
• Ignore all chests from now on. Complete this level as normal.

5. Heartless Abyss

• You've got lots of health so just go crazy
• The important bit here is speed and taking damage can be faster than being precise
• The difficulty in this level is controlling the anchor, constantly be moving to control it's movement and throw it over obstacles.

6. Adept Co. Labs

• Charge + Explosive Punch allows for grenade jumps, so use it to skip certain small sections
• Missiles are good here for UNLIMITED POWER!
• Seriously, just spam the fire button once you grab Farrah Day.

7. Would You Date A Super Villain

• Mash buttons. I use E on keyboard AND B on Xbox 360 controller to mash through text
• During "MASH BUTTONS" sections I mash W and E on keyboard and B and A on controller, all at the same time.

8. Rattletrack Rails

• Umbrellas take one hit
• Train mounted cannons take three hits
• Small trucks take five hits (hence the two ammo upgrades)
• Dynamite-half-tracks take nine hits
• Raijin takes 20-30 hits (I've never counted it properly)
• The train at the end takes five hits (confirmed by OreoPlaysThings)
• Small trucks have a small sound effect that plays when they spawn off screen and you can see their exhaust smoke while they are off screen, with these indicators you can kill them before they even shoot at you once.
• There is a death warp possible towards the end of the level. It needs further testing. It seems to involve dying while throwing an axe at a checkpoint. Happened to me by accident in my PB and can save significant time.

9. Bramble Flats

• Try not to choke the run
• Charge + Explosive Punch allows you to skip small sections
• With only 3hp this is definitely a difficult level, tactical deaths after checkpoints can help with safety (but are ultimately slow)
• After jumping over the first cannons don't climb the ledge to the upper-left. Jump to the far right wall and die in the oil. Death Warp. Health refilled (improving consistency) and it saves around 3s. On 1.0 it causes the Taddle Bots to spawn.
• Lots of enemies in this level means lots of ammo refills drop. Don't be stingy with missiles.

10. Doom Howitzer

• Phase 1 - Mash through text. Do nothing/shoot occasionally
• Phase 2 - Mash through text. Do nothing/shoot occasionally, do NOT move in phase 2
• Phase 3 - Mash through text. Shoot Mack ten times to win. Time stops on final hit on Mack.

[section=Extra Tips]

• Pause and reset after the text box closes on the Sovereign to skip the level unlocking screen. Does NOT work when unlocking Heartless Abyss. Does NOT work on 1.1.
• If you have 6800L at the end of Sukochi then you can play a new vinyl in the jukebox for 200L. "Turn-Based Tussle" is very conveniently placed on the Sovereign if you need to do this. This is of course slower but is a decent backup strat.
• Practise grenade jumps. They can save time everywhere, especially when you manage to chain them together. Check out the IL leaderboards to see where they're useful.
• Practise. Do IL runs to practise certain sections and then come back to the full game runs. Breaking the run down into smaller parts will ultimately improve your overall skill level and improve your full game runs!
• There's nothing wrong with taking a break from speedruns if you're getting frustrated. Nefarious will still be there when you come back to do more runs later :P

[section=Further Discussion] You can chat with the Nefarious speedrunners in the #nefarious-speedrun channel of the official Nefarious discord, or chat with fellow fans of the game in any of the channels! https://discord.gg/eupNX7b -NOTE- The Nefarious Discord server is family friendly, if you can't handle that then don't bother joining it.