There are three ways to obtain Deputy Beagle's journal. After you obtain and read the journal you will advance to the next stage of the quest: heading to Novac through Nipton.
Free Deputy Beagle. After this, if you have a Speech skill of at least 25, you can convince him to help you clear out the rest of the hotel. If you speak to him before you exit the hotel and offer to give him a gun you will open up his inventory. There you can take his journal. Note that this is the only way to obtain the journal without accruing negative Karma.
Kill Deputy Beagle and loot the journal off his corpse.
Pickpocket the journal from Deputy Beagle. Doing this after you free him will cause Negative Karma, but if the note is pickpocketed before he is freed will not cause Karma loss.
It's also possible to obtain the next location by threatening the deputy with a Speech skill of at least 40.
You'll find only two people, the rest have been either killed, or tortured and crucified by Caesar's Legion.
Go into the store on the left to find the second survivor, Boxcars, who tells you that they took a few hostages, and that you need to go to Novac. Speaking to him about this opens up the quest Booted. You can also gain Karma by giving Boxcars Med-X.
Lastly, Vulpes Inculta addresses you if you approach the town hall. He will tell you to spread word of what they have done, giving you the mission Cold, Cold Heart. An important thing to note is that if you brought Boone as your companion from Novac prior to visiting Nipton, he will start attacking the legion regardless and they will turn on you, rendering Vlupes hostile and unable to be talked to.
(Note: Caesar's Legion Fame can be gained when speaking to Vulpes Inculta about the events that happened at Nipton. Proceed through the dialogue asking what happened until given the dialogue to agree with the method that Vulpes used. Upon agreeing the Caesar's Legion fame will be achieved.)
You can complete this quest at any time by simply going inside the The Tops Casino and finding Benny there.
The holotape on Manny/his diary entry is from someone called McMurphy, and the building you find Jessup has the corpse of McMurphy at the back of the room, it's an easy way to get a Great Khan disguise.
If you are vilified with the Legion, Vulpes will attack you on sight and you will not be able to receive the quest Cold, Cold Heart.