/ AbstractSubmillimeter and millimeter wavelengths provide a unique view of the Universe, from the gas and dust that fills and surrounds galaxies to the chromosphere of our own Sun. Current single-dish facilities have presented a tantalising view of the brightest (sub-)mm sources, and interferometers have provided the exquisite resolution necessary to analyse the details in small fields, but there are still many open questions that cannot be answered with current facilities. In this report we summarise the science that is guiding the design of the Atacama Large Aperture Submillimeter Telescope (AtLAST). We demonstrate how tranformational advances in topics including star formation in high redshift galaxies, the diffuse circumgalactic medium, Galactic ecology, cometary compositions and solar flares motivate the need for a 50m, single-dish telescope with a 1-2 degree field of view and a new generation of highly multiplexed continuum and spectral cameras. AtLAST will have the resolution to drastically lower the confusion limit compared to current single-dish facilities, whilst also being able to rapidly map large areas of the sky and detect extended, diffuse structures. Its high sensitivity and large field of view will open up the field of submillimeter transient science by increasing the probability of serendipitous detections. Finally, the science cases listed here motivate the need for a highly flexible operations model capable of short observations of individual targets, large surveys, monitoring programmes, target of opportunity observations and coordinated observations with other observatories. AtLAST aims to be a sustainable, upgradeable, multipurpose facility that will deliver orders of magnitude increases in sensitivity and mapping speeds over current and planned submillimeter observatories.