The year is 1991; one year since an unidentified flying object bearing 300,000 enslaved aliens, the Newcomers, landed in the Mojave Desert on planet Earth. Los Angeles later becomes their new home. Matthew Sykes (Caan), a police detective, loses his partner Bill Tuggle (Brown) in a shootout. The detectives were trying to stop two Newcomer criminals murdering another Newcomer named Porter at a grocery, in what appeared to be a robbery.
The next day, Sykes' superior Captain Warner (McCarthy), informs his squad that they will have to work with the newly promoted Newcomer detective Sam Francisco (Patinkin). Although biased, Sykes enlists to work with Francisco to investigate a similar homicide with a Newcomer named Warren Hubely; feeling that if he investigates that crime, he will also find opportunities to investigate his partner's death which he is officially forbidden to do.
While unobtrusively trying to establish a connection between the two cases, Francisco at a crime lab detects an abnormality on the body of one of the Newcomer criminals who was killed in the robbery. Later, Sykes and Francisco are led to a nightclub to investigate a link in the killings with a Newcomer named Joshua Strader (Kober). However, they end up interviewing his girlfriend instead, after he is murdered by a criminal ring led by Newcomer businessman William Harcourt (Stamp) and his henchman Rudyard Kipling (Howard).
Harcourt is in the latter stages of launching advanced plans to exploit the alien race by attempting to mass-produce and sell a drug called Jabroka. The drug was used in the past to pacify the Newcomers when they were slaves, but has no effect on humans. The abnormality noticed by Francisco on the body of the Newcomer criminal earlier, was a visual sign of the drug's influence. In addition, the Newcomers Hubley, Porter and Strader were involved in the planning phases of the operation, but were later murdered due to Harcourt's desire to exclude them from any future financial rewards. Ultimately, Sykes and Francisco track down Harcourt, where he is secretly negotiating a timetable for a release of the potent narcotic. The detectives attempt to foil his plans, as they are later led on a car chase with Harcourt and his cohort Kipling, through the streets of downtown Los Angeles. Following a head-on collision where both parties are injured, Harcourt attempts an escape on foot. Sykes pursues and corners Harcourt onto a desolate drawbridge. Harcourt then purposely overdoses on a sample of the stimulant.
As Sykes mistakenly believes he died, Harcourt is taken away by an ambulance, but later mutates into a significantly larger and more muscular Newcomer intent on causing violence. The duo pursue Harcourt, catching up with him near a fishing pier. Sykes later ends up in a physical confrontation with Harcourt in the open sea. Harcourt dies, as his body disintegrates due to the effects of direct contact with salt water, which is hazardous towards Newcomer physiology. Francisco commandeers a police helicopter, and rescues Sykes from the water. With the Tuggle and Newcomer murder cases solved, the authorities dismantle Harcourt's illicit scheme.

Question: Why does Sykes partner with Francisco?
Answer: To ivestigate the homicide of William Huberly, but also to search for his partner's killer.
Alternative answer: because his superior, Captain Warner, has ordered him to