I did this for the Witness - it really helped to think out some of the puzzles if scribbled possible solutions down. Oh and Obra Dinn to an extent - mostly things like 'I saw this guy hanging around in this memory - could he be X'?
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Seconding the witness
Yeah, I did this for the witness sort of. If I got stuck on a puzzle and was finishing up a session, I'd take a photo and then draw over the top of it as I went about my day, so I'd come back to the game with a solution.
Myst and its mainline sequels, especially Riven will generally require pen and paper for almost all puzzles (except for the godforsaken train tunnel puzzle). Cyan has also made Obduction which is very similar and I ended up using pen and paper to take notes for. Quern: Undying Thoughts is a Myst-inspired game that is also like this.
the Submachine series by artist Mateusz Skutnik also benefits from using pen and paper, although a few of the games include virtual notes as well. The later games in the series are more open ended and require you memorizing coordinates if you don't take notes. It also helps to write down which items you collect (potentially) go to which screens. It's a 2D point and click adventure game series.
I came here to say "Any Cyan game", Riven i think was definitely one of the most complex and needed the most notes. They've recently released Firmament and Riven remake is on its way too.
Just checked out firmament. Looks very cool.
Return of the Obra Dinn
This was my first thought as well.
I'm trying to put it in a way that won't spoil clues for those who haven't played it yet, but I ended up with plenty of notes and even took screenshots of the ship maps to scribble notes on.
God I wish I could forget all about it and play it for the first time again.
Came here to mention this. I had so many clues and mysteries I was trying to keep track of that I was regularly jotting down notes
This was going to be mine as well. The fact that you don't start to investigate the mystery in chronological order turned out to be quite a treat, as I need some way to organize my thoughts.
Fantastic game, honestly, I've had quite a few good detective experiences the past few years that nearly perfected the genre to me.
Factorio
Gotta keep track of production balance somehow..
In the same vein, Satisfactory and Dyson Sphere Program. I love planning and optimizing and it feels great to plan it on paper then build it in the game, only to run into countless problems, distractions, and rabbit holes of things to do to achieve my goals, requiring taking countless more notes to keep track of it all. Definitely one of my favorite genres of games.
Satisfactory is the first game I thought of. It even made me craft little 2D building models to plan proper factory layouts.
Welcome to my favorite genre of game!
As they've already been mentioned before, I will second both La-Mulana (and though not mentioned, it's sequel), and FEZ.
The Witness didn't make me break out Pen and Paper, but it was definitely one I had to give my brain a break and come back to to look at things from a fresh angle.
Now for some previously unmentioned finds where your attention to detail will be rewarded. Not all will require notebooks. But there puzzles hidden in all of them.
Environmental Station Alpha is a Metroidvania.
Full Metal Furies is a side-scrolling beat-em up.
INSIDE is a side-scrolling platformer.
Inscryption is a deck-builder / puzzle room.
Secret World was a great modern horror MMO for a while there, and the investigation missions had some really complex puzzles that expected you do go online and do research into Egyptian dynasties and King James bible quotes and all kinds of other stuff. They dumbed down the amazing build system the game started with, but the core story skills still all be worth playing.
Elite Dangerous. People have guides on how to do things like earning money fast, but those methods usually require a lot of thinking and planning with a notebook.
RIP EDDB
Subnautica forced me to draw a proper map. It was interesting.
Pretty much any 90s point and click adventure game made by Lucas arts, Sierra etc. No objective marker, no journal, you just wander around clicking things trying to mash items together. “Where did I see that symbol before?? flips through notebook Oh right!”
I'm going to hijack and offer a specific example: Shivers. In addition to having puzzles with clues and inputs spread apart, it also offers a Flashback system that saves important pieces of information that you've already seen (Though actually taking notes is all but required since you still have to tab through the books then go back to the actual puzzle, and some clues are just images placed throughout the museum) The game just oozes atmosphere and tension with the changes in soundtrack and all the writing and environmental storytelling not directly related to puzzles. Once you know all the game's tricks, it does kind of take the edge out of the horror aspect, but even decades later it's still just a treat to walk through the museum's virtual exhibits.
Available on GOG right now, I suggest giving it a try, although do save your game often, as it's Win95 era.
Original Metroid.
Only 2 games that really made me break out pen and paper.
Myst 3 and Final Fantasy XII (The Great Crystal).
Yes, the crystal! I still have the scribbles of my map I drew back then. I loved the feeling to get "lost" in there.
I just got my notes out a month ago because someone was sharing their FFXII collection. It has so many switch names, one-way markings, and strike-throughs where I messed up and realized I went in a big circle. I'm so glad I didn't use a guide for that.
The new System Shock remake. I needed to draw a map of all elevator connections because Citadel station is extremely convoluted. Also, you get codes (or parts of codes) and instructions here an there, that you'll need later on.
No notepad, but an excellent explorative puzzle that had me making and remaking theories the whole time: outer wilds. Several people also mentioned obra dinn
Keep Talking and Nobody Explodes has an entire manual that you should print out and put in a binder, and your manual monkeys will absolutely need pen and paper to help you defuse the bomb in front of you
It happened only one time, when playing Final Fantasy X, I really wanted to know what they were saying before finding all the Al Bhed primers. So I found a few NPC, took notepad and using a few letters found in the beginning, I was guessing what they were saying. It was quite satisfying and helpful, albeit easy.
This, and for the various secret passwords scattered about. “Kilika and Bikanel join as one”.
I did that at one point too. There was a newspaper that I used to get that had a game that did the same thing. But I can't seem to find it now.
System Shock 2. Just the perfect amount of non-handholding and thinking required without being cryptic or tedious.
Oh man, last one that made me do that was probably Zork III. I was hand-drawing my own maps to navigate that game. I miss those days.
Not quite the same puzzley aspect but check out etrian Odyssey. It's premise essentially is that you have a dungeon crawler and you have to make the map yourself. There are tools in game for making the map as you go.
I'm playing through the Switch re-releases now and they're great. The mapping controls leave a lot to be desired versus the DS originals, but it was never gonna be as good as that magic.
La-mulana. It's one of those games that only has value if you play it blind and without a walkthrough. The game's platforming and combat is subpar at best and atrocious at worst, but the riddles and the mythology make up for it. I played it around 2008 on the "MSX" freeware version, and it took me 10 months and 2 new save files after getting stuck. You have no chances of completing that game without extensive notes.
A bit different but The Painscreek Killings. You're a reporter investigating an abandoned village where years ago a couple of murders happened. There is no set ending to the game, you can leave at any time and answer a bunch of questions to see how much of the mystery you have solved correctly, a bit similar to what Obra Dinn does. Until then you can more or less freely walk around (there's a rough order enforced by keys and hints) and figure out what's important. I've filled close to 20 pages with notes, relationship diagrams and a few sketches and still feel like I've seen maybe half of what's there.
EverQuest! I was pretty young back then, but I remember EQ not having a quest tracker back in the day. You'd talk to NPCs and have to keep track of what they were asking for.
I took that goddamn boat and ran for hours to get my warrior armor only to have no idea how to give the quest item to the centaur guy. I gave it to him and he just said "thanks". It was brutal, but kinda hilarious in retrospect.
Honestly, Elden Ring. I kept a small notebook on the side to write down all the different bits I didn’t want to forget. Clues and quests and stuff like that. There were so many things if you pay attention and take care to try to piece together. It was really fun to come across something many hours later and then pull out the notebook to find my notes on it.
Dishonored 2!
Not the whole game, just a single level where you can avoid killing and sneaking by solving the Jindosh riddle.
Oxygen Not Included. Gotta compute the rate at which dupes consume resources to adjust production. It's so hard yet so satisfying. The dupes are extremely stupid though
Since you already said Tunic, I'll throw out Riven: The Sequel to Myst
I played it several months ago for the first time and my desk was completely littered with sticky notes, most of which would have been incomprehensible to anyone else
Tunic is a BIG one. The language puzzles, and the math puzzles. SO MANY NOTES.
I play a lot of old point and click games, and many of them are much easier with a solid note taking practice integrated into my play.
I don't think anything will ever beat Ultima IV for me in this regard.
Voices of the Void.
Writing down the dish names and codes for the reports is a lot more fun than I thought.
I play Ocarina of Time randomizers using both a tracker and my own notes. That game is pretty huge, especially when things are shuffled around.
I take a lot of notes while playing PvP games. Now for TFT.
Signalis. Retro horror game with a really messed up plot; I had to write down radio codes and door diagrams in order to remember them.