Little is known about the Engineers' history beside them being transcendent beings, but the Engineers are shown to be the "creators" of the human race as they visited Earth during its primordial state, whereupon the lone Sacrificial Engineer ingests an unknown liquid, causing his entire body structure to dissolve and seeding the planet with his DNA, and hastening evolution upon that world. The Engineers continue to visit Earth multiple times to secretly observe the human race's development, presumably to pursue further unknown studies on humanity.
At some point approximately 2,000 years before, the Engineers stationed on LV-223 initiated a plan to wipe out humanity for reasons unknown by releasing the black liquid pathogen they had created. However, they apparently lost control of the pathogen and led the Engineers there to die off. Four surviving Engineers took refuge within their ship, storing themselves within its hypersleep chambers; however, only one of them survived.
In 2089, archaeologists Elizabeth Shaw and Charlie Holloway discover a star map among several unconnected ancient cultures within a cave during their expedition on the Isle of Skye. They interpret this as an invitation from the Engineers rather than a warning to stay away. Shaw then contacted Peter Weyland, the elderly CEO/Creator of Weyland Corporation, for a proposal in order to gain enough funding for an expedition to follow the star map. Weyland agrees with the proposal and funds the creation of the scientific vessel Prometheus to follow the map to the distant moon LV-223.
In 2093, after the USCSS Prometheus' two year voyage, the ship arrived on LV-223. The Prometheus crew explored the moon's surface where they came across the Engineer Temple. The crew entered the structure and discovered the bodies of some Engineers, as well as several Steatite Ampules stored within the structure. The crew's interference caused the pathogen stored within the Ampules to melt, a few crew members were exposed to the pathogen, and in the ensuing chaos most were killed. The android David successfully found the last living Engineer and informed Weyland, who was secretly aboard the ship the entire time. Weyland and his team went to the Engineers' ship to commune with the last Engineer however, upon waking; the Engineer decapitated David after a brief conversation and killed Weyland along with the entire party, save Shaw, who managed to escape.
The Engineer reactivated his ship and headed for Earth to carry out his original mission to wipe out the human race. The remaining crew later sacrificed themselves and the Prometheus to destroy the Engineer's ship. The Engineer survived and attacked Shaw within Prometheus' lifeboat, Shaw released the Trilobite she had extracted earlier from her womb as the result of intercourse with Holloway who was infected by the pathogen, which restrains and impregnates the Engineer while Shaw escapes. The Engineer later died and birthed a Deacon.

The Deceased Engineer.
In 2122, while returning from Thedus, the USCSS Nostromo was diverted to the Zeta II Reticulisystem, the Nostromo's onboard computer, MU-TH-UR, intercepted a distress beacon originating from LV-426. The crew members were awakened prematurely from their hypersleep, and they responded to the beacon and took the Nostromo to the planet. A three-person survey crew explored the planet's surface where they came across a crashed derelict ship. Upon entering the ship, they discovered the remains of a fossilized Engineer wearing a Bio-Suit and over numerous eggs that were stored within the ship's cargo bay. Afterwards Kane was impregnated by a Facehugger and was taken back to the Nostromo for medical treatment, only to die a few hours later when a Chestburster bursted violently out of his chest. The creature quickly matured into an adult and began killing the crew members one by one and led to the destruction of theNostromo.
57 years later, the terrafroming and research colony Hadley's Hope established on LV-426 was given a vague order from Weyland-Yutani executive Carter Burke to locate the derelict, having learned of the ship's location from the claims of the Nostromo''s sole survivor Ellen Ripley. Surveyors Russ and Anne Jorden located the ship, Russ was attacked by a Facehugger and Anne pulled him out and radioed for help. Some of the rescue party also went into the derelict and were attacked. All of the victims were returned to the colony which eventually led to its downfall.
A team from Weyland-Yutani later returned to LV-426 nearly five decades later. They recorded the flight telemetry from the vessel, and used it to track down LV-1201, the last planet that the derelict had visited before crashing. On the planet, the company discovered Engineer ruins infested with Xenomorphs; it is presumable that the Engineers were breeding the creatures there before withdrawing from the world. Weyland-Yutani set up an extensive research complex on the planet dedicated to studying both the Xenomorphs and any Engineer artifacts recovered. Much later, while trying to escape the planet with his squad, Andrew Harrisondiscovered a large chamber containing a dead Engineer.
Origin of the Crash on LV-426
The Engineer's remains were first discovered in a derelict spacecraft as crewmembers from the Nostromo were investigating the source of a distress signal emanating from LV-426, (now known as Acheron) an unsurveyed satellite (at that time) that orbits the gas giant, Calpamos. Not much is known on how the Engineer's ship crashed or what it was doing with the Xenomorph Eggs in its hull, but there are several theories:
An Engineer was carrying Xenomorph Eggs as weapons secured in a compartment covered by an electrical mist that reacted when broken, but one of the eggs "hatched" and a Facehugger managed to get out and ambush the pilot by surprise. With the Facehugger attached to its face the pilot was unable to maneuver the spaceship, and it crashed onto the middle satellite (LV-426) that orbits the ringed gas giant planet Calpamos. The pilot, who later gained consciousness, sent out a distress signal but it didn't make it and the Chestburster killed it.
Behind the scenes
"The Pilot" was so named by H. R. Giger, who originally designed the creature. It has become more popularly known as the "Space Jockey," a name that first appeared on a storyboard for the scene in Alien during which the creature first appears.[3] Director Ridley Scott has admitted that he doesn't know who had christened it as such, but the name stuck and became the unofficial moniker for the creature on set.[4]
Alien
The derelict ship contains several thousand Alien Eggs. It is suggested by Ridley Scott in the director commentary to the film that the Space Jockey's ship was an "aircraft carrier or battlewagon of a civilization, and the eggs were a cargo which were essentially weapons. Like a large form of bacterialogical/biomechanoid warfare." The eggs, which are kept in the ship's hold, could presumably be dropped on an enemy planet, and the Aliens would proceed to kill the population as they spawned. "The Space Jockey was...the driver of the craft who is now, after many ages...has started to look like a perfect example of...where does biology end and technology begin, because he seems to have grafted...into what essentially was...a pilot's seat. But clearly from here, this is where the communication attempt would emanate from probably in an automatic transmission. So this creature obviously had experienced, maybe one of the eggs had been disturbed and a creature had got out, had attacked the rest of the crew...but let's say he was a part of the civilization he came from and now had melded into his seat." The Nostromo's computer, Mother, starts to translate the Space Jockey's transmission and it appears to Ripley to be a warning.
According to James Cameron, the Space Jockey's craft picked up Alien Eggs and the pilot became infected by the dangerous cargo; the ship landed or crashed on LV-426 and the Space Jockey transmitted the signal as a warning.
Prometheus
In a 2011 interview with Filmophilia.com, director Ridley Scott revealed that Space Jockey in Alien is actually a suit containing the deceased being (which is never shown). Scott also revealed that his desire to explore the unaddressed story behind the ship on LV-426, the host of eggs aboard, and the mysterious pilot were his primary inspiration for returning to the franchise with Prometheus