Because so many people are having trouble with the mod site, and because the site seems abandoned and it could probably just die off on any given day, I went ahead and downloaded every mod and tool included in this guide and uploaded them to Google Drive, MEGA and OneDrive. Everything is included in a single folder, and you can just pick and choose if you want to download things individually, or just download everything at once. Steam automatically deletes MEGA links, so if you want to use it, remove the <REMOVETHIS> from the link below.

Google Drive: https://drive.google.com/drive/folders/1NpnyfllbRo08YQ9L0aT78E0ublvL8zLO?usp=sharing

MEGA: https://meg<REMOVETHIS>a.nz/folder/O4hCgIJC#yZvtRmaGHp84BAm-uW3gUQ

OneDrive: https://1drv.ms/u/s!AqT47NglLDFwgp0tIUc5MU8Ioi4-SQ?e=VxEb3H

Reminder: everything linked from here on can be found in any of the three storage sites mentioned above.

First, go to http://www.justcause2mods.com/ and download a mod that you like. To download mods in there, you need to create an account. A good one to start of with is the Increased Grapple Range & Speed:
https://justcause2mods.com/mods/increased-grapple-range-speed/

Now that you have your file, extract it to somewhere. Go to your Just Cause 2 folder (C:\Program Files (x86)\Steam\SteamApps\common\Just Cause 2) and create another folder inside it called "dropzone" - without the quotes. Go back to your extracted file, copy and paste it inside the dropzone folder. Voila! Now just start your game with your fresh new mod!

-Sometimes, 2 mods may have the same files. How to install both of them?
Just use this tool:
https://justcause2mods.com/mods/mod-combiner/
* Special thanks to [SpireDev] 1_dylan for the info

-How to unistall mods?
Simply delete the mod files.

Please remember to rate this guide if you found it helpful.

Here is the list of mods that I use and recommend:

Reminder: every mod and tool linked here and above can be found in any of the three storage sites mentioned in the first section of this guide.

-Increased Grapple Range & Speed
https://justcause2mods.com/mods/increased-grapple-range-speed/

-Disable annoying sounds
https://justcause2mods.com/mods/disable-annoying-sounds/

-Desert Eagle - What the pistol should have been
https://justcause2mods.com/mods/desert-eagle-what-the-pistol-should-have-been/

-Chaos Parachute as default
https://justcause2mods.com/mods/chaos-parachute-as-default/

-Air Combat - iNcreasd Air Traffic
https://justcause2mods.com/mods/air-combat-increasd-air-traffic/

-No Blackmarket Cutscenes v2
https://justcause2mods.com/mods/no-blackmarket-cutscenes-v2/

-HD Improved Clouds
https://justcause2mods.com/mods/hd-improved-clouds/

-HD Moon+Stars
https://justcause2mods.com/mods/hd-moonstars/

-Black Market All And Free
https://justcause2mods.com/mods/black-market-all-and-free/

-Can't stop the factions
https://justcause2mods.com/mods/can-t-stop-the-factions/

-Less psychic police
https://justcause2mods.com/mods/less-psychic-police/

-Triggered Bombs V2 with Damage
https://justcause2mods.com/mods/triggered-bombs-v2-with-damage/

-JC2 Map Viewer (Updated) - Not really a mod, but very usefull!
https://justcause2mods.com/mods/jc2-map-viewer-updated/

None of the mods listed here lag your game.


Enjoy!

With the Multiplayer Mod already on Steam, likely a lot of questions regarding the multiplayer and the mods are going to pop. So, to make things very clear: the Multiplayer Mod DOES NOT load mods. You can leave your mods right where they are, there's no need of deleting them, but they won't have any effect while playing MP.