What was the source? How did the virus jump from Africa to the U.S.?
The source of the U.S. outbreak was a female monkey, captured in Africa and illegally transported into the US. When Rudy Alverez (Daniel Chodos), the pet shop owner, refused possession of the monkey because he wanted a male, the monkey was set free near Cedar Creek, California. Unfortunately, the monkey passed the virus to both Rudy and to Jimbo Scott (Patrick Dempsey), the monkey's deliverer. Jimbo then flew to Boston where he kissed his girlfriend, and they both died hours later without infecting anyone else. Back in Cedar Creek, the virus was passed to a lab technician when a vial of Rudy's blood exploded in a centrifuge, and the lab technician spread it during a coughing fit at a movie theater. At this point, the virus was transmitted by direct contact, e.g., Rudy was scratched by the monkey, the lab tech was sprayed with the blood, the droplets of the technician's spittle landed on people around him. The virus subsequently mutated, becoming airborne, and was, thus, passed to other patients in the Cedar Creek Hospital via the airducts.
Once Sam and Major Salt (Cuba Gooding Jr.) learn that the host is a monkey smuggled in from Africa, they frantically begin searching for her before Operation Clean Sweep is carried out, but have to go on the run since McClintock has discredited them to prevent Sam from finding a cure and ruining his plans of covering up the virus. They break into a TV station and go on the air showing a picture of the monkey and asking to hear from anyone who has seen it. A viewer remembers a drawing that her young daughter Kate made of "Betsy", a monkey she says has been playing with her in the backyard. Her mom immediately contacts the CDC. They notify Sam and give them her address in Palisades. Sam and Salt fly their helicopter to the Jeffries' house, where they attempt to get Kate to coax Betsy to come out of the woods. When Betsy shows up, Salt shoots her with a tranquilizer gun. Unfortunately, Lt Col Briggs (Dale Dye) intercepted the call from the CDC to Sam, and McClintock is also on his way to Palisades. When Sam contacts Ford, the only thing Ford can do is to delay the bombing and warns him of possible resistance heading his way. McClintock intercepts Sam and Salt on their way back to Cedar Creek and orders them to fly to Travis Air Force Base or be blown up, but Sam refuses. Salt manages to outmaneuver McClintock's aerial squads and get Betsy back to Cedar Creek where the antibodies in her blood are mixed with E-1101 to create an antiserum against the mutated strain of Motaba in time to save Robby. Ford tries to get McClintock to call off Operation Clean Sweep, but McClintock refuses, still wanting to keep the Motaba virus a secret. When Sam finds out that the bomber is on the way, he and Salt intercept it in their helicopter and try to convince the pilots not to drop the bomb. When McClintock orders them to stop listening to Sam and carry out their mission, Ford briefly explains over the radio what they could do to interfere with the bombing much to McClintock's surprise. Salt bears down on the carrier threatening a head-on collision while Sam still tries to explain on the airwaves that they were purposely not told everything on what was going on. While hearing Sam's pleas, the pilots drop the bomb anyway, but over water, not over Cedar Creek. When McClintock orders the pilots to return for re-arming, Ford relieves McClintock of duty and places him under arrest for withholding vital information from the President having seen that McClintock's actions have gone too far, though McClintock swears he'll make sure that Ford goes down for the crime with him. In the final scene, all of the sick residents of Cedar Creek are recovering, and Sam and Robby make up.
What is the beginning of the movie supposed to show...where they bomb the encampment in Africa?
That scene, which takes place 30 years prior to the setting of the movie, is supposed to show that Major General Donald McClintock (Donald Sutherland) and Brigadier General Billy Ford (Morgan Freeman) knew from the getgo that the Motaba virus had the potential of being made into a biological weapon, since they were the ones who recovered it when it first appeared 30 years earlier. They ordered that the encampment be bombed as they flew away in their helicopter. Under McClintock's plan, it was their goal to obtain a sample of the virus and then wipe it out completely so that no one but the U.S. Army had control of it.