Stone had a leading role in many important discoveries such as the observation of the B+, B0, and Ds mesons. In 2000, he pushed to convert CLEO into a charm factory, which subsequently led to the measurement of the charm-decay constants fD+ and fDs. These measurements demonstrated the applicability of lattice-QCD calculations of hadronic effects in the weak decays of hadrons with a heavy quark with precision of a few-percent, thereby enabling similar calculations to be used with confidence to interpret key measurements by other flavour-physics experiments worldwide. At CLEO, Stone led the design and construction of new high-performance Th-doped near-4π CsI calorimeter detectors. This was the first application of a precision electromagnetic calorimeter to a general-purpose magnetic spectrometer. He also worked on design and construction of a Ring-imaging Cherenkov detector providing four-σ K-π separation over the full accessible momentum range.
In 2015, Stone was involved in the discovery of the pentaquark at CERN. Five-quark resonances, called pentaquarks, were predicted at the dawn of the quark model but were only found after 50 years when Stone and a small team of colleagues uncovered their existence in the LHCb dataset.
In 2021, Stone was part of a LHCb team that unexpectedly discovered the exotic narrow double-charm tetraquark (T+cc, ccud), a type of long-lived tetraquark, in experiments conducted at the Large Hadron Collider.