Ultimately you will always have more than enough room to build your base, so don't panic. For the sake of this guide, it's written from an Emma playthrough. Emma is the hardest to play, in that her super power is basically just being able to do more schemes. Max and Ivan sit pretty with gold and combat bonuses, and will have an easier time. Because there's an achievement for playing all four on hard mode, you will eventually have to do them all anyway.

Play on the third island, the doughnut, because it makes all agents come from the same direction. You can play as any genius, though. Otherwise many of the super agents will come out of the depot instead of the casino. This makes the game MUCH HARDER, while having them come through the casino makes them far more predictable.

Your number one first step is to build a long corridor and place your control room at the end of it. The game makes it sound like you don't want to instantly build a bunch of repeaters but you do. Right now, each repeater is mostly costing you energy; so you should build your power facility next. Try not to do any missions if you can help it; instead go for the optional objectives and reject anything you can't do, because these objectives are random and infinite. You need any source of income you can get in order to do three things:

• Expand the power plant/control room until you have 23 bandwidth, allowing you to have every single region of the world unlocked at once. We're going to need a LOT of gold to make this work.
  
• Build a barracks big enough to place lockers until your at the maximum minion cap of 300; we are going to need the base full of workers in order to defend ourselves. Leave the majority of them as workers, only training minions for schemes and the 50~ technicians you'll need. If you over-train, you will be stuck in a constant loop of making 300k just in time for the day to end and for it to instantly get paid out to your minions (who will then desert the lair because their morale drains at a constant rate)
  
• Expand the base out to take advantage of all the room you have, you want to put some distance between the cover operation and where the majority of your base is; keeping in mind that folks need access to your helipad.

When it comes to what rooms we need in what size, keeping in mind that we simply need to plan it out and not build it all quite yet:

Huge 50x50+: Control Room, Power Room(s), Vault, Training Room. Besides technicians, nobody really needs to go inside these rooms and thus we can safely make them big with a bunch of items in it. The Training Room of course is the exception, you will build it small at first and then expand it every time you unlock new minions. You only need 2-3 trainers of each type, and 7~ tech and guard trainers.

We are going to need a special power room that is dedicated to 10+ incinerators. The longer you let bodies sit in your lair, the more it's going to freak out your minions. This is also why we want to avoid having out security funnel also be our main path, we can't afford the constant drain of desertions if we can help it.

Big 20x20+: Barracks, Cover Operation, Staff Room, Armorey. You will need a barracks in the middle of your base for sleeping and one crammed in the corner full of lockers to raise your capacity. You'll want a security setup so that when intruders get to your bottleneck you can have all your muscle minions charge them at once. Keep in mind that they will always use guard tables first, so if you build too many they will ignore your advanced guard posts.

Big enough to fit the furniture in: Everything else. For the most part the other rooms are going to be built the bare minimum size that they need to function.

We want our base to be sprawled out and cenetralized at the same time, if that makes any sense. Agents shuld have to walk very far in order to get to your Sanctum, but a minion should easily be able to leave their post and regenerate their statistics. This means you might have several staff rooms and barracks around.

Side Stories come in three flavors: Super Agent, Crime Lord, and Loot. Super Agent missions require research you can't do yet, Crime Lord missions throw waves of enemies at you that you might not be able to handle, and Loot objects seem to drain your stats and clog space. To top it all off, the game only can offer you X side stories at once, progressing in the main story causes more side stories to appear but once offered THEY ARE NEVER OFFERED AGAIN; meaning that if you ignore side stories for too long you will be rapidly losing them forever. This bug only became apparent to me at the end of my playthrough. So if you plan on doing them all, you need to ignore the main quest until you have finished the side content otherwise you can softlock yourself out of it.

Out of the handful of characters the game offers as your first Henchman, Jubei is easily the best one in the game. He deals around 50 damage a hit, can teleport like he did in the first game, and his flow ability let's him solo any super agent in the game. Just windwalk, pause to turn on flow, and watch Jubei destroy his enemies. As far as I know, Jubei is the only character in the game capable of dealing the sheer damage that he is capable of.

So knowing we're always going to pick Jubei first, who else do we need? It depends on how tough your security is! Just make sure to avoid people like Sir Danial until later, because he is particularly dangerous on hard mode. Just keep in mind that you will have to fight any Crime Lord you didn't do the missions for at the end of the game all at once in one wave, so it's worth a little of your time making sure you have thinned out a few of them. However, temporary partnerships do count for this; any henchmen you didn't recruit fully but still have in your base won't attack you.

Jubei: His recruitment quest involves a lot of fighting and research, yet he gets offered at the start of the game. You should always pick him, as he is the strongest henchman in the game.

Incendio: This guy causes a lot more problems than he fixes. His quest involves him destroying your entire casino floor and causing problems for you; so you will probably be executing him later to make room for better characters. His only neat trick is that his ranged attack is an AoE stun, kinda nifty but it also seems to destroy furniture.

I.R.I.S.: Her recruitment quest involves several waves of robots that explode in flames when killed, so do be careful. She has a good ranged attack, and her abilities are very useful.

Janet Bombe: I recruited her and sort of forgot her. Her quest was not that tough, she hardly seems to do damage, and her abilities seem useless at best.

Ming: Her ability to release gas is very useful, and her recruitment quest isin't particularly tough.

Sir Daniel: His quest involves him going on a psychotic rampage inside your base. Because of reasons, his infinite ammo bolt action is fully automatic and he will tear through your base. The game bugged out so I never got to actually recruit him fully.

Eli Barricuda Jr.: He fights with his fists for low damage, but can equip his revolver to fire six powerful shots at enemies. He's not bad, but he's also not that good either because of his reliance on babysitting.

The Jewel Theif: I never got the chance to use him, but those who do reported that he does 5 damage a hit and both of his abilities are completely useless. One places a mine that never seems to go off, while the other is a fake painting that rogues can steal.

The Tank Helmet Lady: I never got to use her.

The Archeologist: I executed her the very second she was recruited. Her abilities looked boring, and I needed the room for people that could fight.

Fugo the Assassin: She is the second most useful. She is a great melee fighter, unlocks special schemes on the world stage, and in general is worth the time and effort to recruit.


Super Agents, on the other hand, can't be defeated until you have biologists (and in some cases, Quantums) anyway so you might as well not even bother with it until the very end of the game before triggering the finale. Just like crime lords, you will have to fight every super agent you didn't kill at once at the end of the game; so you might want to do 3/5 of them if not all of them.

Loot objects, for the most part, are not worth it. You need them for the main story, but that's about it. They don't do a very good job of restoring morale, though some of them do actually provide you benefits like extra stats.

Lair: The very, VERY first thing you need to do is research stairs so that you can srpawl out to every floor of the lair. Your basement is probably where your vault and power center will end up being, and you can move the rooms you barely use to other floors so that your base is optimized for minion travel. Again, we want to avoid making minions walk too far to get to a barracks or staff room.

Besides that, we need the improved power generators and vault racks.

Covert Operations: Obviously, we will need the intel desk, advanced repeater, network upgrades, and ideally the second we can research the globe, we get the globe. While the globe clogs the space of four advanced repeaters, it does create intelligence as well.

Minions: Your #1 goal is to have the morale and vitality upgrades, keeping in mind you have to build atleast one of that building for the effect to work in addition to healing that need for that type of minion better. But what we're 100% after is the Vitality upgrades for Muscle and Workers, once you have those two researches, the game is basically over for the Agents. Once they can't one shot your minions in combat, you are able to easily swarm them down with pistols.

We're also going to need pistols along with the deception security tag. Once researched, tag your entire lair with deception, that way agents get stopped in the casino but also get murdered by security in the lair because they attack deception minions that interact with them insides the base for some reason.

Ideally every time a agent gets into your base, they will kill a deception minion infront of a security camera. This will send every stationed guard (preferablly with a pistol) in response to automatically deal with them. By tagging your entire base, you ensure that Agent X and Symmetry will always get caught by your security. Even though they won't get caught directly, they will aggro when their squaddies do and probably get beat up in the process. This is why we don't really care, at all, how much heat we're generating or if we trigger super agents.


Traps: For the most part, traps are kind of useless. Some of them do a little damage, but to be honest I feel like after my playthrough they just killed minions that were deserting more than anything else. You need some of these traps in order to finally kill some super agents, which you can just neatly stack up outside your prison as needed.

Our general goal on the world stage is to always have every single part of the map at the highest upgrade level we can get it. for this goal, we're going to need a grand total of 230 Bandwidth at the end of the game.

Muscle missions get you small chunks of gold quickly, while science missions get you a lot of gold slowly. Because super agents will be constantly raising the heat in your regions, we actually want to focus on military missions more than we focus on the science missions. This is because your science minions will end up costing you a LOT of gold in salaries, while guards are dirt cheap. Deception is 100% useless, the minions cost a lot of gold and are incapable of creating it. You're better off paying for heat loss, or just using the super weapon.

We're also going to want to recruit Fugo, she unlocks special schemes that allow us to decrease heat for free and make some serious gold. But the general idea on the world stage is that we want to avoid hiring too many specialist minions, and always be generating more gold than we are spending.

Something you HAVE TO REMEMBER: The more you upgrade your criminal networks, the more heat they store. This means that the game will spawn tougher enemies when it's that nations turn to send people. Honestly, all this means is that they have more hitpoints. The standard strategy of waiting for your guards to pounce and then finishing them off with Jubei should get you through anything they send at you.

Every Agent has the same behavior, every time. They will appear on the world stage within their jurisdiction (Except Steele, who operates worldwide) and if a scheme is pulled off infront of them, they will visit the island. For some of these agents, we don't really care if they come; others are a bigger hassle. As always, Jubei can windwalk ANYWHERE, pop Flow, and destroy any super agent in a few hits provided you have other minions around preventing them from just shooting him.

Agent X, Super Investor: He will spawn somewhere near the middle of your base, inside, with a squad of elite investigators. Typically, these agents will quickly get caught by a patrolling henchmen or guard and not get very far. Agent X himself places "Planted Evidence" that as far as I can tell exists for other investigators to find. I consider X to be pretty harmless by the time you have 30~ pistol guards, even though he is armed with twin magical shotguns.

Symmetry, Super Rogue: She spawns directly in your vault, fills up her pockets, and then wanders farther into your base to get caught by security. Nobody in her team carries a gun, so it's not that hard to get rid of them.

J. Steele, Complete Joke: A mysterious woman is sending hapless fools pretending to be John Steele after us. They show up alone at the casino and then wander in like anybody else. Steele agents have no particular strength besides being able to kill a minion in one hit for 50 damage, and are usually focused down by security fairly quickly. They have the easiest of the Agent removal missions, in that you just have to gun down a swarm of Steele posers. You can pretty much ignore Steele, knowing that they can't really hurt you.

There are a few acheivements for capturing Steele. Emma can mock them, you can throw them to the sharks, after capture you can have your genius kill them for the achievment, etc.

Wrecking Bola, Super Saboteur: Armed with a big warhammer thing, she has the ability to break doors without a cooldown or animation. However, nobody in her team carries a gun so she is probably going to get gunned down by your security team.

Blue Saint, Super Saboteur: He both is and is not one of the most dangerous agents; because if you don't watch him very closely he is going to destroy your entire base with planted bombs. Thankfully, Saint is the weakest fighter out of all of the agents once caught. He comes in through the casino like everybody else with sabotuers, and is unarmed.

Atomic Olga, Super Soldier: Shockingly, the Super Agent that spawns with a team of soldiers is the most dangerous out of the six. She'll storm the base with a team and begin gunning down everybody in sight once they step inside the base. You need to let your security team engage first and then bonk her with Jubei. She is armed and EXTREMELY dangerous. Out of everybody, this is the super agent you DO NOT mess with unless you know you can handle her.


Agent Items
Super Agents have items that they will randomly place throughout your base through some form of dark magic. Some of these items seem to spawn magically without the agent even being present, while others are obviously placed by the agent in real time. Check your floors and walls every now and then for abnormalities

Camera Blockers: Has a conical white light coming from it. Symmetry seems to place these near where she pops up.

Listening Devices: Placed on the wall, emits a blinking red light. I don't know who places these, they seem to appear everywhere at random.

Fire Bomb: Blue Saint will drop these in rooms while sneaking around. They will constantly set things around them on fire until removed.

Planted Evidence: The tooltip says that Agent X is planting these around, but honestly this seems to just magically appear all over the place. Investigators get suspicion from them... I think.

• Early Game, Scientists:
  This is your initial setup phase, and ends once you have Stairs and Jubei. We need to get to 300 minions fast, the only thing that is going to be stopping agents is huge walls of expendable goons along with your genius as support.
  
  
• Mid Game, Biologists:
  By now your entire base has been laid out. You have a designated vault and power room in the basement, a control room full of repeaters on the upper floors, and roughly 100 of your minions should be paid specialist, gold permitting. Keep doing main missions until you have Biologists, then research everything you can while keeping your gold income beating expenses. Our goal is to upgrade every single network, and top up your research. We also need those minion vitality upgrades, and should consider getting the 230 bandwidth you need to upgrade your networks to max later.
  
  Once you unlock slot machines, use them to build a large maze in the casino while limiting how many deception minions you have. During my playthrough, the agents typically waste a little time exploring the casino and then try to find the base. By stretching out their pathing with slot machines, we can both slow them down and create situations where a super agent gets split up from their team in different rooms in the casino. Once split up, Jubei warps in and takes care of it.
  
  
• Late Game, Quantums:
  The entire tech tree is ours to research now. The first priority is to have a cloning vat so we have both our guards and workers with 100HP. Once you have that, you're unstoppable. Next step is fusion generators. This is when you want to start killing all the super agents, dealing with the extra crime bosses, etc. Maybe upgrade to rifles?
  
  
• The Finale:
  The very second you redeem the quest where you issue the world ultimatem, you have stopped your ability to do side quests and now are on track to end the game. You will have to fight off agents at first, and then fight any remaining characters you didn't kill or recruit yet. The crime lords will show up first, if any are left; same with the Super Agents. Aferwards, you can safely start laying off your specialists to the bare minimum as we enter WORLD DESTROYING MODE. We are going to nee a lot of intel to keep our coffers full and our fuel topped while we blow up provinces.
  
  In total it will cost.... 69 Fuel to destroy the entire planet, so make sure you keep the tank topped up as you go. You will be losing passive income as you blow up the world, so keep in mind you will need increasingly more money to keep the lights on. Realistically, you just have to blow up the five agency bases and the game is over; but we spent a LOT of time to get here so why not enjoy it?