Ellen Ripley was infected by an Alien embryo that escaped from Newt's body following the crash of the EEV (Emergency Escape Vehicle) on Fiorina "Fury" 161. The creature entered Ripley's mouth and subsequently nested within her.
The Inception of Infection
Ripley's infection occurred under dire circumstances, immediately after the devastating crash of the EEV carrying her, Newt, Hicks, and Bishop. This incident set in motion a chain of events that led to the gestation of a Queen Alien embryo within her.
The Crash and Its Aftermath
Upon the crash landing, the EEV sustained significant damage. Newt's hypersleep tube was compromised, flooding with water and leading to her drowning. Since the Alien embryo required a living host to survive and continue its life cycle, it was forced to seek a new one.
The Alien's Path
Following Newt's demise, the Alien embryo escaped through her mouth. Driven by instinct, it then swam towards Ripley, whose own hypersleep tube had also been shattered during the impact. The embryo proceeded to force Ripley's mouth open and crawled into her esophagus, thereby initiating the infection. This invasive process is specifically why Ripley experiences a sore throat early in her ordeal, a subtle indicator of the Alien's presence.
Symptoms and Implications
The presence of the Alien embryo within Ripley's body had profound implications, not only for her but also for the inhabitants of Fiorina 161. The subtle symptom of a sore throat hinted at the terrifying reality of her internal passenger. This infection marked a critical turning point in her enduring battle against the Xenomorphs.
For further details regarding the events leading up to this point, you can consult resources such as the Alien³ FAQ on IMDb.