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helping Contreras - Meeting with Issac at the Gun Runners
If you want to get the very nice rifle, This Machine, you will need to either investigate Contreras and find proof of his smuggling (as covered in the linked article) or help him continue his operations. Note that the benefit of helping Contreras is that you keep Contreras alive and free as a merchant. He has a very nice selection of ammo and weapons and will give you a bit of a discount after the quest is done. It's a long walk to get to him though.
In order to start the quest, you will need to apparently be above level 12. At that point, you should be able to either pay him 50 caps or use 50 points in Speech to get him to open up about his smuggling operations. After he explains his sources, he'll note that he could use a mercenary and he'll hire you.
Your first mission is to go to the Gun Runners and talk to Issac. He's the man who usually stands around by the reloading bench by Vendortron. Unfortunately, something is very odd about Issac's schedule. If Isaac isn't by the reloading bench, follow the road to the east. You'll find two houses that you can go into at the end of the road. The first is the Hostetler home. Isaac's is right behind it. Note that if you approach it or go inside, it's possible that Isaac will run out and sprint back to his spot at the reloading bench.
If you go inside and he's not there, try going back to the reloading bench and waiting for a few moments. You may see him running down the road.
Regardless of how you get him to show up, talk to Isaac and give him the new order. He needs 100 pieces of scrap metal to make the guns. This includes things like pots and tin cans, and I believe that the nearby Aerotech Office Park should have enough all by itself inside the suits. You'll have to steal them, but this shouldn't be a problem.
You can also just skip this step if you have 80 points in Speech or Barter. Regardless of how you get the order to go through, walk back to Contreras and report your success.
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Helping Contreras - Medical Supplies
Your next step will be a simple pickup from Blake at the Crimson Caravan Compound. He should be manning the little stand at the center of the camp. Just talk to him and get the medical supplies. With 25 points in Science or Medicine, you can note that these supplies would make some very powerful drugs.
Doing this allows you to get a 100 cap bribe from Contreras as extra payment for being involved with his drug running operations.
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Helping Contreras - Killing Keller
After you drop the package off, you will need to wait for at least 24 hours to advance the quest. Kill some time, or just wait, and report back for the final part of the mission. You need to go talk to Price at Miguel's Pawn Shop in Westside. You can get to it easily by walking through the west entrance to Westside.
Go inside to find a man named Keller sitting at Price's spot in back. The short answer is that he's an undercover operative building evidence against Contreras. If you give him the passphrase, he won't know the answer. You can just say goodbye and report the problem to Contreras, although it ends up playing out the same. If you give him the package, he'll try to arrest you. You can convince him to let you go with a bribe, although that just maintains the state of limbo. If you want, you can just kill him now.
There is no real way to end this other than to kill Keller. It is possible to turn on Contreras, but that will just result in the same quest as “Investigating Contreras." You still have to hack the terminal and you won't be any better off than if you had just turned him in normally.
It is possible, but difficult, to turn Keller, but there doesn't seem to be a benefit. You won't get This Machine if you don't kill him.
I managed to do this by resisting arrest. I drew my weapon and immediately went into VATS and shot Keller in the head three times with That Gun. This was apparently viewed as a stealth kill, even though Miguel was staring at us the whole time. Apparently you can do this somewhat reliably with a silenced weapon from light cover. I also assume that reverse pickpocketing some C4 onto Keller will work. You can buy some from Miguel and just wait until Keller is standing by himself. As long as you're hidden when you use the detonator, you won't get caught. Just make sure you don't kill Miguel.
Once he's dead, go back to secure your discount with Contreras and claim This Machine as your own.