Error 404 on all other links except Index Page

I used a WordPress Script from Softaculous, a MochaHost Software Service to upgrade my current WordPress platform in hopes that there would be some other cool or secret security add-on features that the host would provide for WordPress

Unfortunately, the script overran the current WordPress I’m using. The script created another fresh WordPress install, deleted my current “index.php”, broke all links in relation to my site and showed off the directory of my site

I uploaded a new “index.php” file from WordPress codex which turned out to fix the Homepage but turned out to encounter this problem in which I’m asking of:

Any suggestions to fix the broken links present on my site?
Should I alter my current database? Or delete my current wp-admin/wp-include folder and upload a new one?

I really have no idea what’s best thing to do right now :'(