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See New San Francisco for details on reaching Navarro. Your main goal here will be to get both the Tanker FOB (see quest #3) and the Vertibird plans so that you may reach the Enclave. The vertibird plans, although not really necessary to reach the Enclave, do make it easier to deal with the various groups in New San Francisco (Hubologists, Shi, Brotherhood) so it's worth it to pick these up while you're here... if only to give them to the Brotherhood to receive a ton of xp, upgrade your stats and pick up the simply awesome YK42B Pulse Rifle at their base. The plans also have nothing to do with the quests so I'll outline how to get them after I explain how to enter.
When you first visit here, Chris, posing as a nobody, will try and prevent you from getting in. Tell him you're just looking around and he should let you go. If you ask about the Brotherhood of Steel or Vertibird plans he'll get suspicious and likewise if you bring party members. It doesn't matter really, but if he does get anxious and go into combat, you'll have to kill him (and probably should anyway) before he alerts the base, and that's something you won't want unless you want to forego any of the quests... still a viable option. Once he's dead, there are a few ways into the underground section, but the easiest is to take the trap door inside the shed behind Chris.
Navarro is really a very simple area to navigate, though it may not seem so when you first get there. When going through the trap door, you'll reach the underground area. Proceed to the northwest section into the locker room to find the very nice Advanced Power Armor and lots of other goodies including a Blue Memory Module. Don't worry about the personnel here, as you'll hopefully be pretending that you're a new recruit and they'll let you be. Otherwise, prepare for a tough fight here and especially, in the base above.
After you're suited up, you'll find all the quests potentially available in the southern middle section of this underground level. Dr. Schreber is the man in the white coat next to a dog on the left hand side. Ask him all about his work and himself, and the deathclaw and dog, and you should pick up both quests #1 and #2. On the right side you'll find a couple scientists next to a computer terminal. Talk to one of them, and if you ask about the base and pass your Speech check, he'll give you the password "snookie" to the nearby terminal. You can also try and hack into it, but it may sound an alarm if you're not good enough. Using this computer can get you a lot of information about the base, and also give you quest #3, which you can also get from the Navarro base cook named "Cookie" when you take any set of spiral stairs.
Now, for the vertibird plans. Make sure you're in Advanced Power Armor and head up one of the spiral staircases. There are two rival mechanics after you take the stairs up to the base. Raul is the one in the Vertibird hangar on the northwest side, and Quincy is the mechanic in the northeast building. The plans are behind Quincy in a locker but he won't let you touch them. First, you may want to find out about their rivalry. Talk with Cookie the cook in the southwestern building and ask him about gossip. You'll get quest #3 and also learn of Raul and Quincy's rivalry.
You can actually make Quincy give the plans to you if you first have the vertibird plan quest (obviously...) and then talk to the technician either in the northern computer building or the southeastern, asking one of them who holds the plans. When you find out that it's the mechanic, talk to Quincy and tell him a tech sent you to pick up the plans. Tell him also, if you found out about their rivalry, that it was Raul. Either way, he'll let you open the locker and retrieve the plans. If you then go to Raul and tell him Quincy wants to speak with him, he'll walk away and ask you to guard the area... which is one way for you to take the K-9 motivator for quest #2.
Quests & Opportunities
Here is a list of some of the quests and other opportunities in Navarro, each with a brief synopsis containing at least one way to solve it. The remaining ways, and possibly other minor quests I will leave up to you.
1. Deal with the deathclaw:
If you enter the underground--the easiest way being the shed behind what likely once was Chris--walk through the long hallways until you come to the junction and then head south. Dr. Schreber is the man in the white coat in the eastern room. Exhaust your conversation choices with him, and tell him you'll kill the deathclaw. You'll first need a Blue Pass Key. You may still have the one from Gecko much earlier in the game, but if not, there's one in his desk. Since it's a soundproof room and he'll stop you if you attempt to take it, you can kill him without alerting anyone and take the key from his desk. Simply try to open the southern door and tell the female guard that you've been told to take care of the deathclaw and she'll allow you to pass. You can talk with the deathclaw inside if you wish, but to complete the quest, use the Blue Pass Key on the southern door.
2. Fix K9:
When you ask Dr. Schreber who's in the underground southcentral room, ask him about the dog and whether or not it can be fixed, he'll give you this quest. The K-9 Motivator is above ground in the Navarro base behind Raul the mechanic in the northwest vertibird hangar. To get it, you must have this quest from the Dr. and you can then tell him he sent you to pick it up... or you can follow the advice above regarding the vertibird plans and take the motivator when Raul goes to take care of Quincy. Use the motivator on K9 and you'll have a new loyal NPC, who won't alert the base while he's with you.
3. Retrieve the FOB from the base Commander:
You can pick this quest up from Cookie the cook in the southwest building of the Navarro base above after exhausting the dialogue choices, or from the Navarro computer in the room to the east of Dr. Schreber's underground, with the two scientists. You can either hack into the computer or ask the nearby scientist if you can use it, and he'll either give you the password or tell you to get lost.
Once you have the quest, the Base Commander is right above the computer room, in the central part of the underground level, in a room guarded by one man. There are a few ways to complete this quest without violence, the easiest being if you have good speech. Talk to the guard and tell him you're here to secure the tanker key, and if you pass the Speech check, he'll let you right in, and the Commander will allow you to go through his lockers and take the key. Alternatively, talk to the guard and you'll learn that the cleaning crew is due in about an hour. Walk away, use your Pipboy to rest an hour, and return to tell him you're part of the cleaning crew. Now enter the room, and either use sneak to lockpick the locker, or use a bunch of Super Stimpaks on the Commander (and wait 10 minutes with your Pipboy) to implode him. Finally, you can bust in, alert the base (if not already on alert) and kill him... which is usually always an option in this game.
Once you retrieve the Tanker FOB and Vertibird Plans, head back to SF and give them to the Brotherhood (your best choice for xp and loot).