This will reset Apple Mail to factory settings.

reset_apple_mail.sh

killall Mail &> /dev/null

# optional, if you want to backup any not-synced data
mv ~/Library/Containers/com.apple.mail ~/Desktop/com.apple.mail.backup

# Attention, these commands will delete everything about Apple Mail except the app itself (factory reset)
rm -rf ~/Library/Caches/com.apple.mail
rm -rf ~/Library/Saved\ Application\ State/com.apple.mail.savedState
rm -rf ~/Library/Application\ Support/AddressBook/MailRecents-v4.abcdmr
rm -rf ~/Library/Preferences/com.apple.mail.plist
rm -rf ~/Library/Preferences/com.apple.mail.searchhistory.plist

# Because of macOS own System Integrity Protection you can't delete this folders with your terminal.
# Open it instead with finder, and delete them.
open ~/library/Containers/
echo "and delete ~/library/Containers/com.apple.mail"

open ~/Library/
echo "and delete ~/Library/Mail"