Warning: Only applies to Atelier Sophie 2. And it’s going to be a really bad Mystery Elixir, in case you found this looking for a guide on Google. Sorry, you’d better continue your search.
For everyone else, this is part 2 of my deep read run of posts on the Atelier series (and I recommend you start with part 1 if you haven’t read it for an overview of the Atelier series if you’re not familiar with it.) I’m still not sure whether it’s part 2 of 2 or of more than 2, but I knew I couldn’t stop with the one post, because I had to take on what to many players is likely the most intimidating aspect of Atelier: all the alchemy. Gathering ingredients, using them to craft items that can be used to craft still more items, with hundreds of properties to choose from and many more effects specific to each item depending upon their elemental makeups. And best of all, not only does each sub-series within Atelier have its own alchemy system that has no relation to any of the others, even each game within those sub-series introduce new elements and remove older ones, requiring the player to learn a new sort of alchemy each time they jump into a new title.
But it’s not enough to just say that: I have to illustrate it. (Do I? Probably not, but I will anyway.) Lately I’ve been playing through the final part of Atelier Sophie 2: The Alchemist of the Mysterious Dream, the direct sequel to the first Atelier Sophie and the fourth title in what used to be the Mysterious trilogy. If that seems confusing, I’ll be writing a review of the game sometime soon to put it into its proper context. For the purpose of this post, we’re not concerned with the why but the how: how to make this fucking Mystery Elixir. And to really illustrate the process, I’m going to write this post in the form of an old-fashioned screenshot Let’s Play. (If you don’t know what that is, I’ve done one before that ended abruptly a few years back; see also lparchive.org for some very old-school examples of user-created playthroughs some of which existed before YouTube.)
Here’s Sophie, our alchemist protagonist, ready to start crafting the Mystery Elixir, a high-level healing item. This or something like it is always featured near the ends of these games to help you out with your final fights and bosses, not to mention the extra/optional ones. I’ve already synthesized one of these, but it’s not a very good one — I can do a lot better.
Starting the synthesis process. Four ingredients are required, one of which is a Dunkelheit, an extremely rare flower that I only have one of, meaning once I make one of these, I can’t make another elixir until I come across another one. (Actually, I can get more of these easily by fulfilling certain requests and redeeming tickets for them, but they’re rare in the wild anyway.)
There’s a problem, however: I want to get particular traits onto my elixir while adding enough of the proper elements to the item to get the most HP recovery and other benefits out of the thing as possible. The best way to achieve this is to synthesize a component item with all of those elements, and the easiest component to use for that purpose is a neutralizer, a sort of liquid… something that can be used in almost any recipe if you’re creative enough.
I’m making a White Neutralizer because why not, it works. But to get this thing to as high a quality as possible, I’m going to want to duplicate a high-level magical item to use in the recipe. It’s time to go to Pirka’s shop.
The Priarco is a craftable item, a sort of crystal pyramid thing. I have no idea what it’s for — in the item’s notes, Sophie says it’s a light manipulation device (a prism?) but I’m not sure what benefit that’s supposed to give to a liquid. But it’s high-quality and cheap to duplicate, and it can be used to make a high-quality White Neutralizer, so who cares. It’s a magical item too, so I guess there’s no arguing about how it functions. It’s just magic, okay?
Speaking of magic, here we see Pirka duplicating this pyramid prism thing.
Also damn, Pirka. If I lived in this dream world (again, I’ll explain when I take on the game as a whole) I’m sure I’d find plenty of excuses to drop by her shop to use her duplication services. Why couldn’t she have joined my party, anyway? I guess someone has to tend the shop, and she doesn’t have any employees.
Time to make the neutralizer. This is the core of the alchemy system in the Sophie games and in a broader sense in the Mysterious sub-series. I think the 7×7 grid is meant to represent the cauldron — in Sophie 1 you could craft new cauldrons and switch them out, starting with 4×4 grids up to 6×6 depending on your alchemy skill and ingredients. Here the range runs from 5×5 to 7×7, and at this point in the game we really can’t do without the full 7×7 grid. You’re also technically crafting “catalysts” this time instead of cauldrons that perform different functions that I won’t even get into here — I don’t fully understand that system myself, but thankfully I’ve been able to get by somehow. I’m using the Limitia catalyst here because it’s the one I currently have that affords me the most flexibility, with the ability to flip and invert pieces to better fit them into the grid.
Anyway, Sophie places every elemental piece of each ingredient in the cauldron in this grid formation, or at least as many as she can manage to fit in. The restricted panels crossed out above can be toggled on and off, but turning them off and having the entire grid free also limits your item growth potential. It’s best to link as many of the glowing nodes of the same element as you can, since that opens up more points to fill on the right side and greatly improves your item. As you can see, we’ve maxed out this neutralizer’s attributes.
Nice work! Now we have a pretty high-quality neutralizer. Could be higher, but it’s fine. Now to move on to the Mystery Elixir.
Just kidding, we have to synthesize still another item first. Often you’ll need to follow multiple steps to get all the good stuff you want onto your resulting item. This can be a pain in the ass, yeah, but it also allows you to customize your items, armors, and weapons and to make them massively powerful. In this case, we can’t directly throw a neutralizer into the elixir, so we’ll have to make an intermediate-step item.
In this case, we’re making a Cure-all Base. Let’s shove a killer bee in there, why not.
Using the cauldron again. And the result:
Sure, that’s fine. Note the traits at the bottom of the item description, all carried over directly from the neutralizer we threw into the cauldron. The item used is important to the final result — my choice of a Cure-all Base was just me being lazy, which I’ll end up paying for soon. But at least I’ve got those nice traits carried over.
Finally, it’s time to make that fucking elixir.
Every ingredient we’ve chosen has been shoved into the cauldron. We’re not even bothering with the lightning element — it probably does something good, but I don’t want that at the expense of what I consider the more important wind and ice attributes: HP Recovery and Auto Activate so that the item is automatically used when the equipping character falls to less than half their HP. Bosses in this game like to take multiple turns and spam massive attacks that can wipe your party out, so this is a (very) partial fix.
Here we’ve got Auto Activate 50%, the best ice attribute we can achieve, but the wind attributes are still a little lacking. I don’t even know what “Activate Split” means, but I can probably get something better than that if I max out the green. So I went back to the ingredient lists… but while I changed Activate Split to Activate Scatter (???) I still couldn’t achieve the top maxed out green attribute. I probably actually can reach it given the right ingredients and the right catalyst, but at this point my laziness overtakes me and I give up. HP Recovery XXL sounds pretty good. This is where my choice of the Cure-all Base might have screwed me over, however: I might have that maxed-out attribute if I’d picked an intermediate item to synthesize with more of the wind element to it. Oh well.
And with these traits carried over from that neutralizer we made at the beginning of the process, we’re looking pretty good now: stronger healing through the Tremendous Healing and Superb Quality traits, and Multiply, which weakens the item’s effect but allows us to use it six times instead of just three. Since inventory space in combat is extremely limited, this is an important trait — we don’t want to run out of uses in the middle of a long fight. And see how happy Sophie is about this synthesis? She’s smiling for a reason: thanks to the setup I managed to put together in the cauldron, with several complete rows and columns, my Super Success Rate rose and activated a massive boost in item quality.
But we’re not done. Now it’s back to Pirka’s place. Yes, I have a legitimate reason for being back here: I need more than one elixir but I’m out of Dunkelheits, and while I can easily get more by doing requests and redeeming tickets at Kati’s bar, that method would also require me to go through the whole synthesis process again, which I don’t feel like doing. Fortunately, Pirka can duplicate my Elixir.
It’s far more expensive to duplicate these, and I end up spending about 80,000 on the job for five of these, but since Sophie 2 lets you spend as much time taking the same requests down at Kati’s bar as you like, money is essentially an unlimited resource. I have far more than I need anyway. I should note that money always carries over to your New Game Plus in Atelier, so it might be in your interest to save up and sell all the materials you’d lose anyway in your new cycle (remembering to keep the gear you want to retain equipped, of course) but I don’t have time for second playthroughs anymore.
Finally, our task is done, so I send Sophie back to the atelier to get some rest. Sleeping in this game doesn’t seem to do anything other than pass time — you can choose what time of day to wake up, and I think certain events or materials might only be available at certain times of day. But since none of the Atelier games have time limits anymore, you can potentially sleep all you want without consequence. I guess the main benefit is getting to see this CG every time (or the equally nice alternate one that I won’t mention because the other character featured is technically a very early game spoiler if that’s even a thing. I’ll save it for that dedicated Sophie 2 post.)
And that’s alchemy. At least, it’s alchemy in Atelier Sophie 2. I mentioned that each game has its own form of alchemy to learn. These are generally, though not always, pretty intuitive to get down. One of the less intuitive systems, at least for me so far, is the somewhat different cauldron/grid format used in Atelier Firis — similar since it’s a game in the same Mysterious sub-series but with some extra elements added in.
Outside of this sub-series, you’ll find totally different alchemy mechanics, however. Like the Material Loop system featured in the Atelier Ryza games:
Or the system from the Dusk series, again with variations between each game. This one is from Atelier Shallie. Is this OK? I’m not sure, but it was the best I could do this early in the game.
Since each of these sub-series takes place in its own universe, it makes sense for them to have different forms of alchemy. It’s a nice way to mix things up as well — the alchemy system would get a little too dull and samey if it were merely repeating, even with slight tweaks, in each successive game. Because alchemy is more than just a tacked-on game mechanic, as I’ve brought up before: it really is at the core of the series. To truly enjoy Atelier fully, I think you have to be at least a little obsessive, willing to mix various ingredients after gathering enough to have a wide variety of types in enough volume to ensure a good mix of traits and high enough quality ratings to make synthesis worth your while.
This usually doesn’t require grinding, either, at least in the way a JRPG would normally demand it. While there’s plenty of combat to be had in the fields and dungeons of a typical Atelier game, many fights can be outright avoided if you don’t want to bother with them by simply running around enemies. This is especially true in the later games, which tend to have enemies that aren’t easily aggro’d unless you really get into their faces. Of course, you can’t avoid all fights: you’ll need to level as you progress, and every Atelier I’ve played has featured a usual lineup of increasingly powerful bosses, some of whom can send you packing back to the atelier to synthesize new armor, weapons, and attack/buff/debuff items.

Especially true for me in Ryza, since I’m not great at coordination and that battle system demands more of your attention with its active element.
However, I’d encourage anyone feeling too intimidated by these complex systems not to be scared off of trying out Atelier. It does require a lot of item-crafting, yeah, but you don’t usually have to go into the kind of depth I do to get S-level items and gear. Hell, I’m not even going into all that much depth — a real series veteran will probably note that my Mystery Elixir still kind of sucks, which I’ll freely admit to myself. For that reason and others (certain rare ingredients only appearing in certain places at certain times, for example) Atelier is one of the few series I’d feel absolutely no shame in looking up a guide for. There are plenty of resources online detailing all the minutia of each game and its items, ingredients, monsters, weapons, and so on. I get the feeling that Atelier was made to please the kinds of completionists and obsessives who are able to put together such guides.
Still, again, you don’t have to be one of them to beat an Atelier game, much less to have fun with one. Though some of the games are more immediately accessible than others — despite being a sequel, Sophie 2 seems like a pretty good title to start with provided you’re okay with a purely turn-based combat system.

And even more ridiculous costumes than usual, but I enjoy those too. What’s with those crystal bunny ears anyway? Naturally, we never get an explanation for them.
That’s it for Atelier, at least for the moment. This series seems to have no end, so there’s always more to say. It’s truly a hidden gem, at least here in the West, where it still seems to get barely any notice outside of the typical fan circles that I move in. More hipster weeb cred for me to enjoy, anyway, if I can really be said to “enjoy” that. Not like I can shoot the breeze with anyone I know in real life and bring this game series up without getting a blank look. Is that a good or a bad thing?
I’m not sure, but either way, it’s my fate now. See you next time!