(Note: you may skip this section if you don't care about my methodology or the other Windows 98 shell options that are not explored in this tutorial)

In this tutorial, we will primarily be using three pieces of freeware (free software): Classic Shell, which is the base shell that allows us to revert our start menu, taskbar, and file explorer design; Resource Hacker, which allows us to modify Classic Shell's internal files to unlock advanced customization options (the Classic Shell website encourages this so don't worry); and Winaero Tweaker, a supplementary program that can enable/disable several Windows 10 features that are usually unmodifiable. I would like to be clear that this is not the ONLY method of achieving our ends - several people have created Windows 98 shells with different software or sheer programming skills - but these are the programs I find most suitable for this specific tutorial.
Now you may be thinking, athorn, WHY are we going through the trouble of modifying freeware that isn't even built for Windows 98 when we could simply pick one that IS? And why must we use three different pieces of freeware instead of just one? Isn't that a bit... inconvenient?
Well for one, I have yet to find a program specifically built for a Windows 98 shell - similar programs such as Start10, StartIsBack, or Open Shell all have built in options for Windows XP/Vista and Windows 7 shells but require tweaking to adapt them for Windows 98 (this is because desktop shells weren't even a thing until Windows 8 came out and replaced the well-loved column start menu with that godawful full-screen app directory). So the question becomes not "which windows 98 shell programs are there?", but rather "which shell program is the most suitable to achieve a windows 98 aesthetic?" To that end, I choose Classic Shell for two reasons: one, that Classic Shell is free and Start10 is not; and two, that Classic Shell is far more customizable than StartIsBack.
But what about Open Shell? To be honest you could achieve pretty similar results with Open Shell, as its creators are the same people as those who created Classic Shell and for essentially the same ends. Further, because Open Shell is still continually updated, it is probably less buggy than Classic Shell (although the only bug I've come across is that my taskbar opacity settings sometimes reset themselves upon startup). But the interesting thing is that Classic Shell remains the more popular of the two - perhaps because its forums offer so many helpful resources for customization and troubleshooting? Or because its longevity alone lends notoriety to the Classic Shell name? I don't know. But I would rather continue using Classic Shell than reformat my entire desktop to accommodate the newer Open Shell.
And if you are concerned about the sheer length and/or complexity of this tutorial, know that 1) I will be including a TLDR at the end of each section, 2) by no means do you have to follow every step, and 3) I am a firm believer in the principle "REJECT MODERNITY, EMBRACE TRADITION", and in the twenty-first century modernity is essentially the fabrication of inconvenience for the purposes of selling convenience. THEREFORE: if you came here for an easy way out of Windows 10's treacherous claws, you are in the wrong place.

The beginning of your desktop's metamorphosis requires no downloads at all - in fact, there are some features which you can enable or disable through Windows 10's built in settings. Honestly, if you want to save some time you can follow JUST this section and ignore all the others, but it will not look like Windows 98 very much at all yet. That said:

1. Changing the Color Palette.

The following is a little diagram I made (in MS Paint of course) to provide a reference for the original Windows 98 color palette. You will be applying a dark blue accent to your desktop through Settings > Personalization > Colors.
First, find the toggle that says "Transparency effects" and turn it OFF, so that all accent colors are opaque (as god intended). Then, go to the section that says "Choose your accent color" and, under the example colors, click "+ Custom color". The custom color you will add is dark blue - specifically, dark blue with a HEX code of #000888 and an RGB code of 0, 8, 136. You can input a HEX or RGB code under the show more arrow of the custom color box. Once you've set that color as your accent color, make sure you CHECK ALL the boxes at the bottom of the page under "Show accent color on the following surfaces". Now, your page headers and active boxes will be adorned with a beautiful Windows 98 Blue :) The rest of the colors will be explored in PART TWO!!

2. Optimizing the Taskbar.

Next, we will be heading over to Settings > Personalization > Taskbar. Some of the settings you will see are open to interpretation, but here are the most vital changes:
The toggle that says "Use small taskbar buttons" must be ON.
The toggle that says "Lock the taskbar" must be ON.
The toggle that says "Taskbar location on screen" should be set to "Bottom".
The toggle that says "Combine taskbar buttons" should be set to "Never".
To remove all those pesky extra features from the taskbar, like Cortana or search, simply right-click on the taskbar itself. You should see a section to show/hide a bunch of random things like the Cortana button or the Task View button (whatever that is) - uncheck ALL of them. You don't want that kind of drama anymore. There are also two additional sections that say "Search" and "News and Interests", respectively; expand both of those sections and then click the option to HIDE the Search and TURN OFF the News and Interests.
That feels better, doesn't it?

HOWEVER! You can go even further than that. If you would like to change your taskbar even more substantially, perhaps by disabling the entire Action Center (that eyesore on the bottom right of your taskbar) or restoring the classic battery/volume control menus, please jump to PART FOUR: OPTIONAL EXTRA FEATURES to learn how to use Winaero Tweaker, yet another fantastic piece of freeware.

3. OPTIONAL Background and Lock Screen Settings.

These settings are just as optional in Windows 98 as they are in Windows 10, so I cannot force you to comply with them. However, if you want to, have fun with the following extras ;)

3a. To change the background, go to Settings > Personalization > Background. You can set the background as a solid color, which would be a teal with HEX code #007d7b and RGB code 0, 125, 123; OR you can set the background as the following PNG image:

3b. The lock screen is a bit tricky as Windows 98 did not have a "lock screen", per se; however, I tried my best to create a sort of hybrid Windows 10 lock screen and Windows 98 startup screen. Under Settings > Personalization > Lock Screen, set the background as the following PNG image:

Then, find the toggle that says "Get fun facts, tips, and more from Windows and Cortana on your lock screen" and turn it OFF; and below that toggle, click on the icons for the detailed status apps AND the quick status apps and set them all to NONE.
If you find that a bit much and just don't want a lock screen at all, you can disable it with Winaero Tweaker, which we will explore in PART FOUR.

3c. At the bottom of the lock screen settings page, you will see a little link to "Screen saver settings". Here, you can have a little fun, but only TWO of the screen saver options available here are also available on Windows 98. Those are "None" and "3D Text". I unfortunately have not found a way to simulate screensavers such as the iconic 3D Maze animation, but please let me know if you do!

the 3D maze screensaver I have in my Windows 98 emulator! Quite ominous... just how I like it ;)

PART ONE TLDR FOR THE REAL ONES
Go to your desktop's settings to change the accent color (Settings > Personalization > Color) to dark blue (#000888 or 0, 8, 136), and disable transparency. Then, change the taskbar (Settings > Personalization > Taskbar) such that tab buttons are set to small and they never overlap. You can right click on the taskbar itself to remove the search bar/Cortana button/etc (and if you truly loathe modernity like me, you can even go as far as permanently disabling Cortana and blocking her from all permissions, which we will explore in PART FOUR). Optionally, you can also change your desktop background (Settings > Personalization > Background) to the Windows 98 default teal (#007d7b or 0, 125, 123) and even add a funky 3D text screensaver.

You've done well to get through the first section of this tutorial, and your desktop is likely grateful to you already. However, the path which leads to your destiny has only just begun. As a reward and in preparation for what's to come, have some 90's background music which was obtained through completely legal and virtuous means:

Now, let us enter the world of Classic Shell.

Classic Shell is an ingenious piece of freeware to which I am eternally grateful. Primarily, it will allow us the ability to transform our desktop start menu from a brutalist app-ridden mess to the original Windows 98 collapsible menu - objectively the superior method of organizing and accessing one's computer programs, files, and administrative tools. However!! It is not quite as simple as downloading Classic Shell. You see, this program has built-in design options for Windows 7 and XP, but we will have to do some customizing to get it to look like Windows 98. (Note: if there is enough demand, I will consider making an additional tutorial for Windows XP and/or Windows 7.)

1. Downloading and Launching Classic Shell.

Pretty simple step that I don't really have to explain because the Classic Shell website does it for me. Hop over there and I'll see you in a bit.

2. Customizing Classic Shell.

Once you have downloaded Classic Shell and allowed it to take over your computer (you can tell this by the sudden disappearance of the Windows 10-style start menu), you will need to open the Classic Shell Start Menu Settings. There are several things we will need to modify right off the bat, so you'll need the following PNGs to start off:

Now that you have those, make sure the "Show all settings" box at the top of the settings window is CHECKED. Now head to the "Start Button" tab and check "Replace Start button" and "Show on all taskbars". You'll have to add a custom button (which is our start button PNG), so click on "Button image" and then click the three dots to select the PNG from your internal files. Make sure that the "Button size" section says "0" and the "Align to corner of the screen" box is UNCHECKED. (Note: if this doesn't immediately work, go to the "Start Menu Style" tab and make sure the "Replace Start button" box is checked and your custom PNG image has been selected.) I'll add screenshots for extra clarification.

And now for the "Taskbar" tab. Check the "Customize taskbar" box and then give the taskbar the following settings: Taskbar look "Opaque", Taskbar color "C0C0C0", Taskbar text color "000000", Taskbar texture set as your custom Taskbar PNG, Horizontal stretching "Tile", and Vertical stretching "Tile".

Almost done! Your taskbar should be looking a lot better already, but the Start menu itself needs some work. Under the "Start Menu Style" tab, make sure "Classic style" is selected. Then, make sure "Replace Start button" is CHECKED and your custom PNG image has been selected. Under the "Menu Look" tab, you can change the width of the main menu (mine is at 30 but I think this is up to interpretation), give the main menu a slide animation as in Windows 98 (I also have the animation speed set to 200), change the Menu caption as you see fit (mine says "Windows98"), remove all font smoothing, and disable menu shadow/glass.

These are all of the most essential settings, in my professional opinion. You can also change the system sounds, customize the items listed on the start menu and their icons (we'll talk more about icons in PART THREE), and change the behavior of the search box - but I will leave this up to your discretion and I encourage you to play with Classic Shell's features.
HOWEVER.
When I implemented Classic Shell on my own desktop, I was frustrated with the inability to customize things like the Start menu's background color and font. Luckily the Classic Shell forums encourage you to use a freeware program called Resource Hacker to edit Classic Shell's internal files - specifically its .skin files - to create a custom start menu skin. You can do this yourself if you're interested and perhaps a little insane, OR you can download the custom .skin file I created myself, named "Classic Custom". You can download this file below and implement it by placing it within the "Skins" folder of Classic Shell's program file (if you don't know where your program file is, simply right-click on any of the Classic Shell executable files and select "open file location"). Then, in the Classic Shell Start menu settings, go to the "Skin" tab and you should now see "Classic Custom" listed under the list of available skins. This should either automatically add a gray background and MS Sans Serif font to your Start menu, or give you the option to change it.

Download Athorn's Classic Custom Skin Here

PART TWO TLDR
Download the Classic Shell freeware program and then open its Start menu settings; here you will be able to add a custom Start button (PNG provided above), change the color and opacity of your taskbar (recommended: #C0C0C0, opaque), change the size and opening animation of your Start menu (recommended: Classic start menu style, menu width 30, slide animation), and various other settings which I will leave up to personal preference. Some aspects of the menu/taskbar can only be changed with a custom skin; you can either create a .skin file with the Resource Hacker freeware or download my custom .skin file above, called "Classic Custom", which primarily changes the color scheme and font of the Start menu. Classic Shell also has settings for file explorer, but I will mostly be addressing the file explorer in PART FOUR with Winaero Tweaker.

Once again - you can stop here if you're satisfied with the changes we implemented in parts one and two. I mean your desktop is probably already WAY better than it was before. But if you're like me, both a perfectionist and a worshipper of aesthetics, then you may still be unsatisfied with some aspects of your desktop... for one, those gross hyper-smooth minimalist icons. Well you're in luck because there is a great wealth of resources available for vintage icons!! I will list several places where you can download them, but keep in mind that they will need to be ICO or ICL files in order to work properly, not PNGs or JPGs. So if they are not ICOs/ICLs, you will need to convert them manually, which is a bit tedious. Or you can download these ICOs that I have provided myself. ;)

1. Icons for Your Downloading Pleasure.

You can download all original Windows icons from this link or this link, or from the ones I've provided below (which are all ICO files, although not every Windows 98 icon is included here sorry I didn't feel like converting all the PNGs lol); I recommend putting all of these icons in a single file that is easily accessible. Also, please note that every downloadable file included in this tutorial will also be compiled under the "Materials for Your Downloading Pleasure" tab to the left, for the sake of easy access.

2. How to Change Desktop Icons.

Now that you've amassed a glorious collection of pixelated mini-masterpieces, you can change the icons on your desktop with two relatively simple strategies.
First, head to Settings > Personalization > Themes. On the right side of the page, you'll see a link that says "Desktop icon settings"; by clicking on this, you'll be able to permanently change the icons associated with the Computer, User File, Network, Recycle Bin, and Control Panel shortcuts. As long as the "Allow themes to change desktop icons" box is UNCHECKED, these will literally never change again (unless you do so yourself).
However, these are the only icons that Windows 10 will allow you to permanently change. So, to change the icons for the rest of your desktop shortcuts, you will need to repeat the following process on each one: 1) right-click on the shortcut and click "Properties". 2) Click "Change Icon..." 3) Click "Browse" to navigate to your custom icon file and select a new icon. 4) Click "OK" and then "Apply", and if necessary, allow administrative access to change the icon.
It is VERY IMPORTANT to note that, if any of your desktop programs update themselves, they may also automatically change the shortcut icon - in which case you'd need to repeat the process once more. Unfortunately I do not know how to prevent this from happening, I'm so so so sorry. But it's worth it.... right? (Note: if you don't like the little arrow overlay that appears on desktop shortcuts, head to PART FOUR and I will show you how to change the shortcut overlay using Winaero Tweaker.)

3. How to Change Start Menu Icons.

Okay, so our desktop is looking nicer.... but what about the start menu? Luckily, Classic Shell has a built in option to customize the start menu's icons, so this part will be very easy. Simply head to the "Customize Start Menu" tab of the Classic Start Menu settings and double-click on any of the menu items on the left column to edit them. Once again, you can click on the three dots to navigate to your custom icon file and select a new icon. These, unlike desktop shortcuts, will change permanently unless you change them again.

Uhh... that's all I got. Unfortunately I do not know how to permanently change a certain program's internal system icon; if you do then please let me know!

PART THREE TLDR
Simply download the custom Windows 98 icons (which should be ICO or ICL files, you must convert them if not) from this link or this link, or from the ones I've provided above. I recommend keeping them all in a single, easily accessible file. To my knowledge you cannot permanently change every system icon in your computer, but you CAN do the following: permanently change your Computer, User File, Network, Recycle Bin, and Control Panel shortcuts (Settings > Personalization > Themes > Desktop icon settings); temporarily change any other program shortcut on your desktop; and permanently change the Start menu item icons through Classic Shell's "Customize Start Menu" settings.

WOW... we have been through a lot so far, haven't we? I almost feel like this tutorial has brought us closer together... I'm kidding I actually have no idea who is reading this. But if you've gotten this far then thank you, genuinely, and please let me know if I've done a good job. This sort of thing is inevitably complex, but I have tried my best to make it easier for you than it was for me.
There is not much else you need to do; your desktop has already emerged from its cocoon a beautiful 1998 butterfly. The only other things I have to show you are nitpicky changes, which is why I've filed them as optional extra features.

congratulations on this new chapter of you and your desktop's life, shinji!

1. Using Winaero Tweaker to Modify System Features.

Winaero Tweaker is a freeware program I recently discovered and I'm INCREDIBLY glad I did, because it truly pairs so well with Classic Shell. It's like hot coffee and cold mornings... or Monster energy drinks and Drum & Bass albums. Anyway - I encourage you to download Winaero and explore all of its remarkably user-friendly features, but I will highlight some of my favorites that are specific to the Windows 98 aesthetic.

1a. Under "Advanced Appearance Settings", you can change the System Font, Message font, Statusbar font, and Window Title Bar font to Microsoft Sans Serif, which is the default font for Windows 98. You could also change it to something weird like Comic Sans, but I don't know why anyone would torment themselves like that.

1b. Under "Behavior", you can permanently disable such evil features as App Lookup, Timeline, Windows Updates, and auto-snapping of windows. You can also restore the original Blue Screen of Death (although let's hope you never have to see it) or enable the Emoji picker hotkey! 😎

1c. Under "Desktop and Taskbar", you can permanently disable the Action Center AND taskbar web search (FINALLY). You can also restore the old volume control panel!

1d. Under "Windows Apps" (my favorite section by far), you can permanently disable Cortana, app auto-updates, and Windows Ink Workspace.

1e. Under "Shortcuts", you can change disable the "- Shortcut" text that appears in the description of all desktop shortcuts and you can also change the shortcut arrow icon to the following beautiful classic arrow (if you haven't already downloaded it in PART THREE):

2. Microsoft Agent Scripting Helper.

Microsoft Agent Scripting Helper (MASH, or just MS Agent) was a program that was implemented in Windows 98 and came built into every OS until Windows 7. The program, though admittedly redundant, featured quirky little animated avatars that popped up on your screen and retrieved files or read lines of text aloud. You could also script special behaviors for them, and on Youtube people have written full cinematic storylines for their MASH avatars to perform. While it is becoming increasingly difficult to find resources for using and customizing Microsoft Agent Scripting Helper, it has a special place in my heart and so I will share with you what I can.
Bellcraft.com is the only place where you can still find any version of MASH; visit their site to download the program. They also have a list of custom MASH characters, but for some reason none of the download links worked for me. So, I used the Wayback Machine to view older versions of the Bellcraft website (which go back as early as 1999!!) and I was actually able to download the character ACS files that way (my personal favorite is Merlin). Let me know if you have problems with this, I know it's quite tricky!
Operating the MASH program itself is also tricky, so I highly recommend both watching the intro tour and looking up some Youtube videos. Currently I have Merlin programmed to automatically appear on startup, tell me the date and time, and then sing me a short rendition of Party Rock Anthem by LMFAO, although it took me weeks to figure that out so don't worry if you don't catch on right away.

3. 3D Space Cadet Pinball.

This is probably the easiest section of this entire tutorial. Quite literally all you have to do is go to this website to download the original 3D Space Cadet Pinball, the best computer game to ever exist in the history of computers.

PART FOUR TLDR
Download Winaero Tweaker, a fantastic freeware to pair with Classic Shell, and gain the ability to enable/disable/customize features like system font, Cortana, shortcut overlays, and automatic OS updates. You can also download the now-defunct Microsoft Agent Scripting Helper from bellcraft.com and 3D Space Cadet Pinball from groovypost.com.