Transmission spectroscopy of transiting exoplanets provides our current best opportunity to study exoplanetary atmospheres, particularly those of smaller exoplanets. However, stellar photospheric heterogeneity due to spots and faculae complicates these studies by introducing spectral signals that can mimic or mask planetary features. The Pandora SmallSat Mission, selected in 2021 as part of NASA’s Astrophysics Pioneers Program, is designed to study the atmospheres of planets transiting active, low-mass stars by disentangling stellar and planetary signals in transmission spectra. Here we provide an overview of Pandora with a focus on the science enabled by its unique multiwavelength dataset. Pandora will observe multiple transits of at least 20 exoplanets with sizes ranging from Earth-size to Jupiter-size and host stars spanning mid-K to late-M spectral types. Pandora will collect long-duration photometric observations with a visible-light channel and simultaneous spectra with a near-IR channel. The broad wavelength coverage will provide constraints on the spot and faculae covering fractions of low-mass exoplanet host stars and the impact of these active regions on transmission spectra. Pandora will subsequently identify exoplanets with hydrogen- or water-dominated atmospheres and robustly determine which planets are covered by clouds and hazes. Pandora’s legacy will be a library of long-duration, simultaneous multiwavelength observations and a catalog of benchmark planets that will aid in target selection and data analysis for JWST and future exoplanet missions. The project is made possible by leveraging investments in other projects, including an all-aluminum 0.45-m Cassegrain telescope design and a NIR sensor chip assembly from JWST. The mission will last five years from initial formation to closeout, with one year of science operations. Launch is planned for the mid-2020s as a secondary payload in a Sun-synchronous low-Earth orbit. This timeline will ensure both rapid scientific results and operational overlap with TESS, HST, and JWST, enabling synergistic studies.