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Stopping the vehicle at the destination will be achieved by reversing the ion engine thrust.
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Ah, I thought so. That means you have to take propellant with you, even though your ship doesn't require fuel That would work, but you should be aware that the amount of propellant required to decelerate from interstellar speeds is considerable. That would increase the mass of the ship in flight, and therefore the energy required to get it up to speed.
A more efficient scheme (once you can set up the infrastructure required) would be to have a beam station at each end of the route, one to accelerate the ship and one to decelerate it. The ship itself needs no on-board propellant at all; you fire small, massive particles (that is to say particles with mass) at the ship to acccelerate or decelerate it. This is a way of transferring momentum to a distant craft. One method (suggested by Isaac Kuo on this forum) is to accelerate innumerable tiny foil light-sails toward the craft; they would vapourise on contact with the ship and impart thrust to it.
Once you have beamstations on all the local stars you can send spacecraft from system to system relatively efficiently.