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 after you free him. This will cause you to gain Negative Karma.
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.
(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.)
On the way to Novac you will get ambushed by several Viper Gunslingers if you travel by the road up the hill. There are 4 or 5 with 2 above you on rocks, and at least one grenade rifle.
He will make you clear out a building to the west, the REPCONN Test Site, before he tells you anything, beginning Come Fly With Me. However if you want to skip REPCONN, just go to Manny Vargas's motel room and check out the terminal in there, it has a file called "Khan Hospitality" which tells you that they are headed to Boulder City. Players can go directly to Boulder City and talk to Jessup or use the Confirmed Bachelor perk to skip this step.
You can use the terminal in his hotel room to read his journal logs to trigger the continuation of the quest, which bypasses Come Fly With Me.
You can kill him and loot the necessary quest item.
You can just steal holotape from his pocket. Either looting or stealing the tape also bypasses Come Fly With Me.
(Confirmed Bachelor) Tell him you can see he's been neglected, and he decides that you're a nice guy. He tells you where the Khans are heading.
You can also speak to Manny Vargas about his co-worker, Boone. Speaking to Boone can open up the quest One for My Baby, making him available as a companion.
Alternatively, instead of completing Come Fly With Me you may kill Jason Bright and his followers at REPCONN Test Site. Returning to Manny Vargas will then allow you to get the needed information.
Manny will then tell you that they went to Boulder City.
Inquire about your delivery assignment with the administrator of the Mojave Express in Primm.
Find Primm's lawman to get information on where your attackers went.
Head to Novac through Nipton. Ask around Novac about your attackers.
Find out from Manny Vargas where the Khans were headed.
Intercept the Great Khans at Boulder City.
You can complete this quest at any time by simply going inside 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".