We categorify the commutation of Nakajima’s Heisenberg operators
$P_{\pm 1}$
and their infinitely many counterparts in the quantum toroidal algebra
$U_{q_1,q_2}(\ddot {gl_1})$
acting on the Grothendieck groups of Hilbert schemes from [10, 24, 26, 32]. By combining our result with [26], one obtains a geometric categorical
$U_{q_1,q_2}(\ddot {gl_1})$
action on the derived category of Hilbert schemes. Our main technical tool is a detailed geometric study of certain nested Hilbert schemes of triples and quadruples, through the lens of the minimal model program, by showing that these nested Hilbert schemes are either canonical or semidivisorial log terminal singularities.