We present a flag manifold based method for detecting chemical plumes in long-wave infrared hyperspectral movies. The method encodes temporal and spatial information related to a hyperspectral pixel into a flag, or nested sequence of linear subspaces. The technique used to create the flags pushes information about the background clutter, ambient conditions, and potential chemical agents into the leading elements of the flags. Exploiting this temporal information allows for a detection algorithm that is sensitive to the presence of weak signals. This method is compared to existing techniques qualitatively on real data and quantitatively on synthetic data to show that the flag-based algorithm consistently performs better on data when the SINR dB is low, and beats the ACE and MF algorithms in probability of detection for low probabilities of false alarm even when the SINR dB is high.