We realize the treatment of bound and continuum nuclear systems in the proximity of a three-body breakup threshold within the ab initio framework of the no-core shell model with continuum. Many-body eigenstates obtained from the diagonalization of the Hamiltonian within the harmonic-oscillator expansion of the no-core shell model are coupled with continuous microscopic three-cluster states to correctly describe the nuclear wave function both in the interior and asymptotic regions. We discuss the formalism in detail and give algebraic expressions for the case of core+$n$+$n$ systems. Using similarity-renormalization-group evolved nucleon-nucleon interactions, we analyze the role of $^4$He+$n$+$n$ clustering and many-body correlations in the ground and low-lying continuum states of the Borromean $^6$He nucleus, and study the dependence of the energy spectrum on the resolution scale of the interaction. We show that $^6$He small binding energy and extended radii compatible with experiment can be obtained simultaneously, without recurring to extrapolations. We also find that a significant portion of the ground-state energy and the narrow width of the first $2^+$ resonance stem from many-body correlations that can be interpreted as core-excitation effects.
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