This guide is meant to help you move forward to complete the game, should you find yourself stuck and not able to advance further down the plot. I was like this for a while, but then I figured a few things out.
There are also some spoilers ahead.
You have been warned.

While you don't need ALL of these blueprints in order to use the rest of this guide, they are helpful in solving your problems (assuming you already have The Scanner):

1. The Repair Tool- the repair tool is relatively easy to acquire, and I assume you will have found it before you continue this guide. If you have not found it, find the Crashfish (the ones that swim towards you and explode), and once the crashfish has blown up, go back to the plant it was living in. Pick up the sulfer, and you will unlock the blueprint for this tool.

2. The Radio- fix this in your lifepod with the Repair Tool, and come back to it periodically to listen to distress signals from other lifepods. Going to these lifepods will reward you with blueprints, fragments, and other goodies.

3. Scanner Room- this room can be found relatively easily, though it takes some exploring to find the fragments. You shouldn't have to go to some of the extreme biomes to locate the fragments, they will be in wrecks around the grassy pleateu and in wrecks surrounding the shallows and the kelp forests.

4. Beacon- this blueprint is incredibly important, and makes it easier to relocate places of interest and wrecks that you cannot fully salvage, expecially for players who do not have photographic memory.

5. Cutting Tool- this is very easy, as there are fragments all over the shallows, kelp forests, and grassy pleateu. This tool is necessary to enter certain areas of wrecks, and to explore the Aurora further.

This room requires a lot of power, but 3 solar panels (not including the ones for your own habitiat) should be plenty to operate this room at all times of the day. Attach it to your base, or give it its own hatch, and enter the room (note: make sure that the room connects correctly, as it only has 2 sides to enter it). On one wall, you should find a panel that has a list of objects that you will recognize; limestone chunks, quartz, metal scrap, even wrecks! Click on one of these items, and the Scanner Room will begin searching for the object you have selected.

I highly recommend getting the Scanner Room HUD upgrade, which can be crafted at the fabricator located only inside the Scanner Room. This will automatically show the locations of objects that the Scanner Room has found, and will always display on your HUD while you are in the Scanner Room's range. This is too useful to pass up.

The Scanner Bots are nice, but they just provide an extra way to explore without going out yourself. These bots just save you time and let you explore without the limitation of your oxygen. If they get themselves around Stalkers, they become bait and are essentially useless.

Note: when you scan for Fragments using the Scanner Room, it will only search for Fragments of blueprints you do not have or are incomplete. It will not show you the location for any Fragments of blueprints you have already obtained. This does help keep your HUD clear of clutter, but sometimes you want to find some Titanium without the chance of Copper taking up inventory space.

In the Shallows, there are a number of giant coral tubes that contain lots of resources. You will want to mark these, as you will want to come back and collect all of its resources, even if you have a Waterproof Locker. You'll also want to take a floating air tube, and some air tubes to let you stay underwater longer. You can skip taking those items if there is a Brain Coral nearby, as you can gather oxygen from its bubbles.

The Scanner Room's range is limited, so you will need these beacons to mark the locations of larger wrecks further away from your base of operations.

If you make some secondary bases (which I recommend, as they can provide you with oxygen and even places to store cured food, or indoor growing planters once you eventually find them). Put these bases and Beacons along routes you happen to frequent or travel to often.

When you find a wreck that has a sealed door that requires the Cutting Tool, and you have not acquired the Cutting Tool yet, place a Beacon there, and add a "C" at the end, to remind you to return to this wreck with the Cutting Tool. Name the Beacon like this:

Wreck 3, C

These wrecks are particularly important, but more on that in the Cutting Tool segment.

These are much more important for a survival or hardcore playthrough than in a freedom playthrough. By the time you have a Seamoth, you don't need these bases for oxygen, but rather for indoor growbeds, to grow food for a quick snack while you're out exploring or traveling between important locations around the world.

These bases don't need anything more than the space for a growbed, a hatch, and 1 solar panel. You will have lighting and air, and food, and that's all you will need from these bases.

In my survival play through, having enough food and water while in the most extreme biomes is always the greateset limiting factor. So I built habitats with growbeds full of Buloba trees, which provide food AND lots of water.

DO NOT use these bases for storage, because then you will have to go all over the place just to find resources that you already gathered.

There isn't much to say about the Cutting Tool, other than you will need it for a couple of times in wrecks, and aboard the Aurora. However, don't neglect this tool, as it will be necessary to find important blueprints and other treasures!

I had to use the Cutting Tool to enter a wreck to find the Modification Station, so build it as soon as you have the resources.

The Cutting Tool requires a lot of power, so bring a spare battery for it (unless you're aboard the Aurora, where you'll find plenty of batteries on board).

While you will likely acquire this blueprint early on, you will not be able to construct the Cutting Tool until you locate the Jellyshroom biome (which you will enevitably find during the story), or when you happen to find the Mountain Island and explore its cave system.

This tool is not something that you will need often, so keep it in your storage at your base until you need it (going aboard the Aurora, for example).

Frankly, if you have the Building Tool, you’re set. You can build any base you want, and make it however you want...
Oh, your base is constantly being flooded. Okay, I can help.

I’ve been amazed by the number of players I’ve seen who do not look into the corner and see that the base they’re building has a number for its structural integrity. They just put down base structures and don’t even plan on it collapsing under the water pressure.

Now that you know that number exists, how can you keep it from going down?
You can’t, that’s just the nature of adding more units to your base.

How can you RAISE that number?
I can answer that question.

The easiest thing you can do is add a foundation to your base. It’s the ugly platform that won’t line up with your base for some reason. It’ll add 2 units of integrity to your base.
Next, once you have the blueprint for it, you can add bulkheads to your base. They’re doors that need only a few cheap materials to make, and add 3 units of integrity.
Lastly, there is the reinforcement wall thingy. It’s a bit more expensive than the other options, but it also is not an eyesore or an inconvenient obstacle to go through.

Power is interesting, as it will draw power from power sources in the order that you build them. If your fuel for the bioreactor is being sucked away too quickly, adding more solar panels won’t solve the problem, power will still be drawn from the bioreactor before it draws from the new solar panels.

Solar- your most basic form of power. I suggest adding around 6 of these to your primary base before adding any other forms of power, as solar is more renewable than the Bioreactor and the Nuclear Reactor.

Bioreactor- the next form of power you will acquire. Once you add Indoor Growbeds to your base, you will have a reliable and renewable source of power.

Thermal Reactor- while this is an infinite form of power, you will have 1/2 as much power available at any time as the Bioreactor will provide you.

Nuclear Reactor- the largest source of power. Use this when you are ready to power the rocket ship and leave the planet.

You should by now have already obtained the blueprint for the Seaglide and made one, and you might have bothered building the Mobile Vehicle Bay and constructed the Seamoth. Let me say a few things about the vehicles:

The Seaglide: you should always have this in your inventory, and on your hotbar (the "2" key is the quickest to press from WASD, so assign it to "2" for a quick getaway from predators!). Keeping a spare battery for it is not a bad idea, though you will be able to keep your Seaglide powered longer with the Swim Charge Fins.

The Seamoth: for me, this is my primary mode of transportation. It is the fastest of the vehicles constructed at the Mobile Vehicle Bay, and the easiest to build. You should be using this vehicle a lot while you explore, as it will provide you with oxygen and protection against predatory sea life.

The Cyclops: this is an excellent mobile base, as you can construct a Fabricator, Battery Chargers, Wall Lockers, and other useful items that you would have in your base. It should not become your new home, as its weakness is that it can easily be attacked by predators, while your stationary base does not attract predators. The Cyclops is powered by 6 Power Cells, and everything that requires power that you place in your Cyclops will draw from those Power Cells, so putting Power Cell Chargers in your Cyclops is not practical.

The Prawn Suit: The Prawn is necessary to advance in the story, as the Seamoth can only go to a maximum depth of 900m without being crushed, with a level 3 Seamoth Depth Module, and The Prawn can go deeper, with the level 1 and 2 Prawn Suit Depth Modules.

WARNING: SPOILER IN THE BELOW PARAGRAPH

To get to the Alien Thermal Power Plant, which is 1200m down, you must have the level 1 Prawn Suit Depth Module, and then you will be able find the Alien Thermal Power Plant and find materials to craft the level 2 Prawn Suit Depth Module.

What I have done in the game is give my vehicles names. My Seamoth is named The Albacore, like the tuna. My Prawn Suit is named The Lobster. And my Cyclops is named The Orca.

Giving your vehicles names makes them more personal to you, and coming up with them is quite fun!

All of the upgrades for vehicles are useful, but all of them are circumstantial, and each of them has their own unique use.

The Depth Modules are mandatory to equip with your vehicles, as they will be necessary to continue the story. And be sure to keep them upgraded, so as to keep up with the depths you will search.

The Engine Efficiency Upgrade is always useful. Use it when you have long distances to travel or many errands to run.

The Storage upgrade is INCREDIBLY useful for the Prawn, especially when mining, though having a secondary storage unit on your Seamoth is also useful, if to a lesser extent.

The Solar Charger for the Seamoth is incredibly useful, as it allows you to keep your Seamoth charged (during the day, and at shallow-ish depths, and with line of sight to the surface) without making multiple Moonpools (which is dumb), or carrying a spare Power Cell.

The Seamoth Perimeter Defense Upgrade is particularly useful, as you will be able to ward off predators who will cause harm to your Seamoth, and will even cause a Leviathan Predator to release you if you are caught in its jaws.

When exploring the Lava Zone, equip your Prawn Suit with the Thermal Charger upgrade, which will give you infinite power while you are in hot water.

The Prawn Arms are separate from the Upgrade Slots, but are very useful, though keeping one arm normal and the other upgraded is recommended.

• The most important one is the Drill Arm, which allows you to mine large mineral deposits.
  
• The Torpedo Arm is useful when fighting monsters, but is not necessary to ward off predators, as punching them can get rid of annoying fish.
  
• The Propulsion Cannon Arm is very nice, as it lets you do everything you can with the Propulsion Cannon in the safety of the Prawn Suit, however it uses a lot of power, even with Ion Power Cells equipped.
  
• The Grapple Arm is quite useful when you do not have the Prawn Thruster Boost upgrade, as it will help navigate areas that your default boosters cannot carry you over.

The Cyclops is my least used vehicle, despite its great potential to be used as a mobile base. You can build lots of things inside of the Cyclops, such as Fabricators, Battery Chargers, and most importantly, Indoor Growbeds.
The drawback that stops me from using it is its clumsiness in piloting it, and the fact that eventually you must return to your original base where there are Power Cell Chargers and replace all of your depleted Power Cells.
While you are able to buld Power Cell Chargers in your Cyclops, they're just draining power from your existing Power Cells, and ultimately will be depleted by the other functions of the Cyclops, such as the lights, the engine, and charging your other vehicles in the vehicle bay.

Even so, you can't go wrong with any of the upgrades for the Cyclops. Every upgrade has its utility, and being able to suppress fires from the cockpit is pretty convenient. Launching decoys to get rid of monsters attacking you is also nice, particularly when you've invested lots of resources into your Cyclops (and especially when it's your mobile base).

One of your first impulses will be to gather up all of the Scrap Metal to be processed into Titanium, but it is the wrong thing to do. Allow me to explain...

In order to acquire Enameled Glass, you need 1 unit of Glass, and 1 Stalker Tooth. As you cannot slay a Stalker (I have tried and failed MANY times) you must collect Stalker Teeth when they feed on metal objects. Occoasionally, they will lose a tooth, much like sharks in our world, and it will drift to the sea floor, where you can then pick it up for your own uses.

Luckily, the Scanner Room can detect Stalker Teeth, and if you have the upgrade to display their locations on your HUD, you can quickly enter Stalker territory, get the teeth, and get out with minimal injury to yourself.

Aerogel is an important ingredient for a number of blueprints and vehicle upgrades. There are two ingreidents to make it: 1 Ruby, and 1 Gel Sack.

Finding Rubies: as you continue to explore around the islands, you will find Rubies deep underwater. They're bright red, so they're difficult to miss, unless you're moving too quickly in the Seamoth.

Finding Gel Sacks: this particular naturally forming ingredient can be found in and around caves in deeper waters. They have a purple glow, but if you're moving too quickly, you will miss these.

Once you are able to find these two items, it will become easier for you to locate more and craft Aerogel for your vehicles and upgrades.

In my most recent survival playthrough, I found lots of Gel Sacks and Rubies around one of the distant lifepods. Make sure you're searching around lifepods, not just the interiors. You may also find wrecks near these lifepods, which will have lots of rewarding loot!

This ingredient is made by combining Hydrochloric Acid and Gold, and is used for a number of upgrades and at the Modification Station.

How does one get Hydrochloric Acid? You need 3 Deep Shrooms and 1 Salt Deposit.

As you explore the other lifepods, you will find one that will be in particularly deep water. Around this lifepod, you will find Deep Shrooms. Collect as many of them as you can (preferably a number divisable by 3), and return to your base. Salt Deposits are easy to find, so you won't have to look far to find them. Then you can craft Hydrochloric Acid, and in turn Polyanline.

Growbeds, once you find them, will become important to your survival and freedom playthroughs.

The most imporant thing Indoor Growbeds provide is the ability to grow land based plants in your base. Most importantly, the Lantern Fruit Tree and Buloba Tree. These two plants are the most valuable to grow, for the purposes of acquiring food and powering your Bioreactor.

Outdoor Growbeds are also valuable, as they will allow you to grow oceanic plants around the relative safety of your base.

I do not have a full list of plants you should grow to harvest, but here are some good pointers:

1. Kelp- makes gathering their seeds easier and safer than going to the kelp forests and dodging Stalkers.

2. Bloodvines- allows you to collect bloodvine oil, which is necessary to craft Benezene.

3. Deep Shrooms- saves you the trip of going that deep to collect them. Slash one with your knife, and you should collect a good number of seeds.

4. Gel Sacks- saves you half the time to crafting Aerogel. Now you only need to find Rubies, and harvest the Gel Sacks.

Those are the Outdoor Growbeds, now for the Interior Growbeds:

1. Lantern Fruit- easiest to use as fuel for your Bioreactor

2. Buloba Tree- provides you with water

3. Chinese Potato- meh, you can grow them, but they're not great.

4. Marblemelons- An excellent source for food and water.

There are 5 ways to collect water.

The first way is to simply find it. You begin with your Lifepod stocked with water, and exploring the Aurora and wrecks will sometimes yield bottles of Disinfected Water.

The second way to find water is to catch Bladder Fish, and use them to craft Filtered Water at the Fabricator.

The third way is to collect Coral Tube Samples and Salt Deposits, and using those resources into crafting Bleach, and then using Bleach to craft Disinfiected Water at the Fabricator. This method is the most viable in the beginning, as it is incredibly easy to do, and can be done in the Shallows without having to stick your neck out.

The fourth way is to use the Water Filtration System. This is an advanced habitat installation, and filters sea water into Salt Deposits and water. This system yields 50 oz bottles of water, making it the largest single source of water available in the game. At advanced points in the game, this is the preferred method to collect water, as you don't even have to leave your base to collect it, and the Large Disinfected Water takes up less space in your inventory.

Note: the Water Filtration System requires lots of energy, but is absolutely worth the effort to construct and power.

Another note: at small quantities, the normal Disinftected Water seems better than the Large Disinfected Water from the filtration system, but becomes more of a burden as the quantities scale up. To carry 150 units of water, you'll need 5 normal bottles, or 3 large bottles. At 200 units of water, it's 6 normal bottles (rounding up), or 4 large bottles. Beyond that, large bottles win out (but you really shouldn't carry more than 200 units of water with you).

The final way to acquire water is to craft the Still Suit, which will passively feed water back to you as you swim around. However, the water from the Still Suit has a small negative modifier to your food count, and sometimes you might forget about drinking it, and then you don't have as much water in your body.

I have completed the game a couple of times, and have done a number of other playthroughs to explore other parts of the world I tend to ignore during my survival and hardcore playthroughs.

If there is something I didn't cover, leave a comment, and I will (eventually) reply and give you my advice!

Waiting time for me to address your comments is between 15 minutes to a week (but normally within a couple of days, hours if you're lucky).

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