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First, let me point out that Kickstart is not a restoration script. It is merely an archive extraction tool. It is not necessary for restoring your backup archive. The actual installation script is always included inside the backup archive.

Now, as long as you have multiple databases definitions, the restoration script (Akeeba Backup Installer - ABI) will always prompt you to restore each and every database which has been backed up. The top section of the script's page will let you know which database is being restored. There is no automated option for skipping the restoration of a particular database.

If, at some point, you want to restore just Joomla!'s database and its files, you will have to do a little manual procedure. First, use Akeeba eXtract Wizard or Kickstart to extract the archive. Before launching the restoration script, edit the installation/sql/databases.ini file and remove all sections except the joomla one. This will instruct the restoration script to skip the other databases.