In this article, we associate to isometries of CAT(0) cube complexes specific subspaces, referred to as \emph{median sets}, which play a similar role as minimising sets of semisimple isometries in CAT(0) spaces. Various applications are deduced, including a cubulation of centralisers, a splitting theorem, a proof that Dehn twists in mapping class groups must be elliptic for every action on a CAT(0) cube complex, a cubical version of the flat torus theorem, and a structural theorem about polycyclic groups acting on CAT(0) cube complexes.