Recently, manifold dynamics has assumed an increasing relevance for analysis and design of low-energy missions, both in the Earth–Moon system and in alternative multibody environments. With regard to lunar missions, exterior and interior transfers, based on the transit through the regions where the collinear libration points L1 and L2 are located, have been studied for a long time and some space missions have already taken advantage of the results of these studies. This paper is focused on the definition and use of a special isomorphic mapping for low-energy mission analysis. A convenient set of cylindrical coordinates is employed to describe the spacecraft dynamics (i.e. position and velocity), in the context of the circular restricted three-body problem, used to model the spacecraft motion in the Earth–Moon system. This isomorphic mapping of trajectories allows the identification and intuitive representation of periodic orbits and of the related invariant manifolds, which correspond to tubes that emanate from the curve associated with the periodic orbit. Heteroclinic connections, i.e. the trajectories that belong to both the stable and the unstable manifolds of two distinct periodic orbits, can be easily detected by means of this representation. This paper illustrates the use of isomorphic mapping for finding (a) periodic orbits, (b) heteroclinic connections between trajectories emanating from two Lyapunov orbits, the first at L1, and the second at L2, and (c) heteroclinic connections between trajectories emanating from the Lyapunov orbit at L1 and from a particular unstable lunar orbit. Heteroclinic trajectories are asymptotic trajectories that travels at zero-propellant cost. In practical situations, a modest delta-v budget is required to perform transfers along the manifolds. This circumstance implies the possibility of performing complex missions, by combining different types of trajectory arcs belonging to the manifolds. This work studies also the possible application of manifold dynamics to defining suitable, convenient end-of-life strategies for spacecraft orbiting the Earth. Seven distinct options are identified, and lead to placing the spacecraft into the final disposal orbit, which is either (a) a lunar capture orbit, (b) a lunar impact trajectory, (c) a stable lunar periodic orbit, or (d) an outer orbit, never approaching the Earth or the Moon. Two remarkable properties that relate the velocity variations with the spacecraft energy are employed for the purpose of identifying the optimal locations, magnitudes, and directions of the velocity impulses needed to perform the seven transfer trajectories. The overall performance of each end-of-life strategy is evaluated in terms of time of flight and propellant budget.