FAT32 (or what Linux calls vfat) has no concept of directory or file permissions. Linux simulates file permissions, but since accidentally executing a file could have undesirable consequences, so execute permission for files is typically disabled by default. But with a mount option you can give all files on the USB execute and write permissions (to also record levels or scores).
Initially (once) you need to create a mount point (you likely already did this):
Then mount the USB partition with fmask that basically gives all files 777 permissions:
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sudo mount -o fmask=000 -t vfat /dev/sda1 /media/usbmem
You can either symlink (ln -s) the path to something on that to your home directory, or create a script in your personal ~/bin that cd
's to the necessary directory and does sudo ./ioquake3.arm
Alternately an /etc/fstab entry could be used to mount it easily, but I need to test to see what would work best for that, especially if that USB device is not always present.