In this article, position and attitude tracking control of the quadrotor subject to complex nonlinearities, input couplings, aerodynamic uncertainties, and external disturbances coupled with faults in multiple motors is investigated. A robustified nonlinear dynamic inversion (NDI)-based fault-tolerant control (FTC) scheme is proposed for the purpose. The proposed scheme is not only robust against aforementioned nonlinearities, disturbances, and uncertainties but also tolerant to unexpected occurrence of faults in multiple motors. The proposed scheme employs uncertainty and disturbance estimator (UDE) technique to robustify the NDI-based controller by providing estimate of the lumped disturbance, thereby enabling rejection of the same. In addition, the UDE also plays the role of fault detection and identification module. The effectiveness and benefits of the proposed design are confirmed through 6-DOF simulations and experimentation on a 3-DOF Hover platform.