The paper presents theoretical and implementation aspects related to a numerical integrator used for the simulation of large mechanical systems with flexible bodies and contact/impact. The proposed algorithm is based on the Hilber-Hughes-Taylor (HHT) implicit method and is tailored to answer the challenges posed by the numerical solution of index 3 differential-algebraic equations that govern the time evolution of a multibody system. One of the salient attributes of the algorithm is the good conditioning of the Jacobian matrix associated with the implicit integrator. Error estimation, integration step-size control, and nonlinear system stopping criteria are discussed in detail. Simulations using the proposed algorithm of an engine model, a model with contacts, and a model with flexible bodies indicate a 2 to 3 speedup factor when compared against benchmark MSC.ADAMS runs. The proposed HHT-based algorithm has been released in the 2005 version of the MSC.ADAMS/Solver.