Data assimilation schemes with empirical background models of the ionosphere are already in operational use. However such methods suffer during disturbed conditions when large gradients are present and are moving relatively fast through the modeled domain. Also, such schemes have limited forecasting capabilities. In order to improve disturbed conditions modeling, more sophisticated assimilation schemes based on sparse measurements for the coupled thermosphere ionosphere system are needed. We have implemented an ensemble Kalman Filter (enKF) for the Thermosphere-Ionosphere (TI) system. We used the Coupled Thermosphere Ionosphere Plasmasphere electrodynamics (CTIPe) model as the background for an assimilation scheme and created the Thermosphere Ionosphere Data Assimilation (TIDA) software package. We published our first paper discussing neutral mass density assimilation during quiet geomagnetic conditions in Space Weather in 2018. In this paper we present results from experiments during the 2003 Halloween Storm, 27-31 October 2003, under very disturbed (K$_p$ = 9) conditions while assimilating GRACE-A and B, and CHAMP neutral density measurements. TIDA was able to simulate this disturbed period without using the L1 solar wind measurements which were contaminated by solar energetic protons, by estimating the model inputs from the density measurements. TIDA is being prepared to offer specification and short term forecasts of neutral density for satellite drag and debris collision avoidance for space traffic management. We also plan to offer long term (solar cycle length), average neutral density estimation for satellite fleet management.