In the phase diagram of elemental boron, an unknown high-pressure form was identified as gamma-orthorhombic boron (gamma-B-28), provoking studies of the extraordinary properties of its main building blocks, B-12 icosahedra and B-2 dumbbells. Although two low-pressure phases, alpha- and beta-rhombohedral boron (alpha-B-12 and beta-B-106), are also composed of icosahedra, the detailed kinetics and mechanisms of the structural transition from alpha-B-12 or beta-B-106 to gamma-B-28 remain poorly understood. We report on new metastable boron phases formed during the transition in high-pressure high-temperature conditions that were discovered using the crystal structure search method. The metastable phases are understood to be a three-dimensional buckled defective honeycomb lattice in which boron vacancies lead to a dynamically and mechanically stable structure with triangular motifs. We suggest that the metastable phases act as intermediate states on the transition pathway from alpha-B-12 to gamma-B-28 owing to their structural flexibility and low enthalpies, in the framework of Ostwald's step rule.