Voyager receives the EMS pulse that Paris sends out after the shuttlecraft carrying him and Neelix crashlands on the planet surface, and thereby are able to get a transporter lock on him and Neelix during the small window of opportunity allowed by the planet's weather conditions.
Food reserves are down thirty per cent of capacity, as the crew have not had the opportunity to re-stock the food stores in weeks. Unfortunately, the planet does not provide any supplies.
Paris and Neelix crashland in a shuttlecraft on the planet. It is unclear whether the shuttle is retrieved when they are rescued, as Voyager only has a limited window of opportunity to remain in the planet's atmosphere and no mention is made of tractoring or beaming the shuttle up to the ship during that time.

Paris and Neelix in the crashed shuttlecraft
Under attack from the alien ship, Voyager suffers minor damage to the port nacelle and switches to the lateral thrusters.
The electromagnetic (EM) disturbances in the atmosphere interfere with transporters and communication.
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