that won't be a problem. As soon as you have collected enough gold nate's restart the world ability will be available for you even as long as nate is gone on a mission.

If you don't progress any further and want to cancel the current objective before, you can abandon single objectives in the campaign menu. In the PC version, click on the objective icon on the upper side of the screen and chose a new objective. You will be asked twice if you really want to abandon the objective.

[edit] Sorry, misread your current objective. In Gardener's Unite, Nate isn't even available in theory. You probably don't have Kiz in his seat, right? Check the Fire Phoenix or Merci the Mad Wizard. Usually one of them has borrowed Nate's ability during these objectives.