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You will often encounter salvaging when running missions. Here are main methods to get rid of it:
1. Politely ask to go away – this may help. But do not be rude, or just shoot immediately, remember that any salvager can always come back on a much more powerful ship than the agent-runner.
2. Withdraw from the mission - a rather inefficient way, and a loss of time, based on the fact that NPCs may kill the compulsive frigate of the unwary novice thief; and on the fact that the salvager will not stay on the mission without the source of income.
3. Leave your NPC centric setups in the pockets - they will shoot the salvagers.
4. You can shoot yourself in your wrecks when a salvager comes close to the wrecks (good against unexperienced players).
5. Take a look at the thief's Employment History. If he is in an NPC corporations, and his toon has generally less than 15 days - is unlikely that he has a powerful ship. You can destroy him, but to be careful, because to kill an agent-runner raven is easy by many ordinary ships. In any case, you should take F.O.F. (cruise missiles) into the mission.
6. You can change your ship for a faster one and catch the salvager yourself with Warp Disruptor I. As the thief have salvagers and the probe launcher, he probably has no guns.
7. A nice way - to kill the salvager's frigate with an industrial ship, which collects the loot after the mission. Install Stasis Webifier I (better II) and Warp Disruptor I on the industrial ship.
8. If you're in a corporation - any co-ally can quickly arrive on an Interceptor and destroy the thief. You can also log in with your alternate account, without being distracted from the mission. Actually, when running missions, you can always take your alt toon on a fast ship (e.g. an Interceptor or Recon) with Warp Disruptor I. Your Alt would fire and at the same time salvage  the thieves.