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Advanced Fluid Handling not terribly important in a vanilla game, but if you're in a modded playthrough it really helps deal with the pipe clutter that generally accompanies more advanced chemistry. Note that the graphics aren't really in Factorio's style, but also don't stick out like some of the placeholders used in other mods.
Alien Loot Economy enemies drop loot, you can make that loot into stuff. Best use is for something like a deathworld. Note that the modules in particular can become OP, and I can't remember offhand if that can be addressed in the settings. Also, you need a way to pick up that loot, especially from turrets killing enemies.
BZ's resource mods there's a number of separate mods here, adding stuff like aluminum and titanium ore. Great for adding a bit more resource variety, but they don't really add new end products (weapons, buildings, tools, etc). Could be nice to combine with vanilla+ mods for a mix&match overhaul of your own creation. Note that adding all of them adds a LOT of resource patches to the game.
Ammo Loader+ pretty much what you'd expect; it'll auto-load turrets from a special chest type. Useful if you're one of those people who likes the idea of deathworlds/Rampant but struggle to set up supply lines in a timely manner. Can also auto-fuel boilers, smelters, etc, so might also be useful for playing a mod with a burner phase.
Autodrive: ever wish your car/tank/modded vehicle worked more like spidertron? This mod allows you to order the vehicle around, get it to shoot enemies automatically, interact with the logistics network, etc.
Change Map Settings aside from the obvious, it also easily allows you to see what your map settings currently are, which is useful if you bounce between playthroughs or took a break.
Cheaper Ammo... Maybe? a fairly small mod that changes the firearms magazines recipe to require explosives, but craft 20 magazines at a time while requiring only a fraction of the metal it would normally cost. And yes, it adds an early explosives recipe that takes ~30 coal. I think it might make ammo a bit too cheap, at least after getting the oil-based recipe. However, it's interesting for combat-heavy runs, and overall I like the idea of making gun turrets a bit more competitive after acquiring flame turrets.
Clean Floor hate seeing weeds and stuff sticking up through your walkways? Yeah, this mod author does too.
Dark Matter Replicators . 18+ To be clear, this is a bit of a cheaty mod that wrecks vanilla balance. You get buildings that can produce items from nothing but time and power, and default "balance" allows for super cheap replacement of vanilla recipes. However, it does have it's own research that is based on it's own unique ore being made into science packs. Again, not really vanilla-balanced but you could use it to make your own version of a Seablock playthrough.
Deadlock's Stacking Beltboxes & Compact Loaders allows you to compress items into stacks, allowing you to move a LOT more items on a belt. However, you generally also need to decompress the items before use. One use is if you use a main bus design but don't want dozens of belts, or if you've outgrown the original design but really don't want to do a major overhaul of it. Note that the compression also means that more items can fit per tile of belt, so it will take far longer for parts of the factory to back up.
Factorio and Conquer: Tiberian Dawn obviously based on the Command and Conquer RTS series, this adds the unique in-universe tiberium resource and things you can use it for. Fairly similar to the Omnimatter mod, except that tiberium is radioactive and patches actually grow on their own. Can be played with normal resources or a special map variation where tiberium is the only resource and you start out with some basic equipment to mine and process it into other raw materials.
Factorissimo 2 adds factory buildings that you can walk into--they're actually bigger on the inside! Optionally, you can actually place factory buildings inside factory buildings. . . Inside factory buildings, that are inside other factory buildings, etc. Like a Russian nesting doll, but if each doll could fit a few dolls alongside each other. At least one of the forks (notnotmelon's) significantly reduces the potential UPS cost for megabase-builders.
Intermediate Bulk Containers a niche little mod, it adds 3 liquid containers that both increase the individual volume carried and also the volume carried per stack. Situationally useful, like if (for whatever reason) you want to move significant amounts of liquids as "barrels" instead of the usual options.
Inventory Repair little mod that just auto-repairs stuff in your inventory if you have the repair packs for it. Convenient, especially for people that like turret creep tactics.
Kills To Science for all the folks who want a direct material benefit of killing biters, and/or hate building out the science part of the factories (you know who you are). It's a fairly balanced way of getting research done simply from killing enemies. By default, it's a pretty small amount of research for the amount of combat, so you could include it as insurance against your tech progress stagnating in the face of severe biter assaults, or bump up the science value per kill and use it as your main method of research.
Kruise Kontrol yes, that's the correct spelling. IMO, a wonderful mod that more people should try out. Basically, lets you put your character on autopilot. Moving from point A to point B is an obvious use, whether walking or driving, but there's more. Mining will selectively target that type of object. In other words, auto-mine coal at the very start to feed your baby factory, clear out tons of rocks or trees, or even objects marked for deconstruction. You can even select ghosts and it will act as a combo of construction bots + automatic assembler for missing buildings. I've found that, at least with Far Reach on, it can even pull resources out of chests to complete the task. However, it can be annoying if you've placed nearby ghosts that you don't actually want to build out yet.
Leighzer's mods he's got a small collection. Science Ores spawns special ores that assemblers can convert directly into science packs, and by default I think it requires the same amount of raw ore than the science pack would normally require. Buried Science skips even that, and mines science packs directly. Both are pretty broken for vanilla play, obviously, so choose mod collections/map settings with care, and don't forget to lie about downloading them to any friends that are hardcore factory builders.
Leighzer's, continued he's got a few other mods of note, including Scrapyards. It adds a new "scrap" ore that can be processed in assemblers to give iron + copper plates, green chips, gears, and copper wire. Kinda neat because it's a "new," somewhat-valuable resource that doesn't actually mess with existing recipes. Leighzer's Morphite is basically an ore that can be turned into other ore types to fill any gaps. Cheetah Ore is a high-performance fuel with very low energy density, but it'll make that car go fast long before you get solid fuel. Also, it can be processed into other some other fuels later on. Lastly, Leighzer's Slow N' Cheap Items makes recipes for miners, inserters, assemblers, etc. that are crafted out of raw ores and have half the stats of whatever machine they are copying. AFAIK the power pole is the only exception, with the same stats as a regular small pole but using just 1 copper + 1 iron ore per recipe. Great for rapid expansion early on, but do keep in mind that without another mod you'll be unable to change the slow ones into something more useful.
Loot Chest UPS you know those mods that drop tons of stuff on the ground from slain enemies? This will collect all of that for you across the entire surface, though IIRC it's locked behind bots and it will NOT pick up loot that dropped earlier. It may seem a bit cheaty to teleport the loot to a central chest, but accidentally leaving loot scattered around isn't a good thing. Aside from the obvious, I'm pretty sure loot left on the ground has a tiny UPS impact and enough of it could cause problems.
Good grief, this is long, and I'm only through the "L's." I'll stop the text wall for now and (possibly) come back to write more later. . . Unless someone begs me not to.
Krastorio 2 ironically used to make it easier.
And then a stooge on SE's Discord got awarded the job of building a tighter integration between K2 and SE in the SE philosophy and went totally overboard on it. And the ongoing feedback in the negative, stating that they were taking it too far, eventually started to be met with swift bans.
Their way, or the highway.
Most of the compatibility lives in the SE post-processing mod, which does its damnedest to run as the very last mod and have the end-say in things. So good luck with runtime patching it back to sanity. Worst-case you'll spend dozens of hours on it, only to have it black-listed on either SE or the SE post-processing mod as 'incompatible with [..]'
https://steamcommunity.com/app/427520/discussions/0/3827539750721369715/
but still, on its own it adds exploration rewards for a vanilla game, with an addon for Krastorio2 - and is a very cool addition imho
Warptorio is a little more extreme in its game changing aspects (as opposed to the complimentary nature of the ruins mod) - but since that's the point it does a great job in turning Factorio into a very different kind of game/challenge
i will also likely be recommending the Story Missions mod in a thread once i play a little more of it to be sure i am well informed - but the first level has all the hallmarks of a fun campaign in the style of the final level (5) of the current demo
Solid mod, absolutely solid.
It gives you additional useful things to launch, with 2 brand new science types to unlock cool bonuses from lab productivity to reusable shuttles in order to reduce launch costs...
It doesn't just adds new tech to unlock new recipes to unlock new tech to unlock new recipes ; no, it's actually useful.
It lets you speed up any boring waiting periods, whilst returning to normal to build and plan.
RTS Units and Total Automization (and RTS controls) Letting you have remote controlled soldiers/tanks and such.
Transport Drones, a very nice earlier alternative to logistics robots that is lightweight, in my experience, on performance whilst also allowing me to set up long range trucking networks to deliver supplies dynamically, fueled with oil or steam if you use a submod for steam.
Yuoki's mods, because besides Pyanodons they have very nice generator mechanics, and a nifty side-tree of development.
Pyanodons total pack if you're a masochist or have a lot of riddalin on hand. I love them but they are ridiculously complex to even build the most simplistic thing such as animal bedding.
Just getting to Red Science production takes hours with Pyanodon...but it is rewarding in it's own way.
Edit: My Number One recommendation after Speed Controls? Factorissimo. I adore having the micro factory buildings, it can feel cheaty, but if an enemy destroys it then it's all gone, so it's not really 'cheaty' imo, it lets you use vertical space essentially. The way it works is that you place down a large structure which is larger on the inside than the outside, and then can build factory connections in/out. I like to use it with recursion/nesting (placing factories inside of factories) disabled so it isn't too 'cheesy' for me.