The Lyman alpha (Lya) forest is the main probe of the intergalactic medium (IGM). The observed Lya flux depends on both the thermal state of the IGM and the underlying matter distribution, and being measured in redshift space, provides sensitivity to cosmology. Traditionally, the Lya forest has been studied using the 3D autocorrelation function to probe large scales and cosmology, and the 1D flux power spectrum to probe small scales, IGM physics, and dark matter. In this talk, I will discuss the Lya cross-spectrum, a hybrid statistic that probes the 3D small-scale correlations in the Lya forest. Thanks to DESI, the dense sampling of Lya sightlines now makes it possible to have robust measurements of the cross-spectrum. I will present measurements of the cross-spectrum at z∼2 − 4 using nearly 800,000 DESI quasar spectra, and discuss the implications for future cosmological and IGM studies.