(The exact dates of Operation Javier are unknown, but based on the game's data files, it can be implied that Operation Javier takes place in the summer of 2002 and right before Resident Evil: Dead Aim.)
American agents Leon S. Kennedy and Jack Krauser are sent to South America to capture the drug lord and leader of the Sacred Snakes, Javier Hidalgo only to discover that the entire village Mixcoatl has been infected with the t-Virus and partly the T-Veronica virus. Manuela Hidalgo escapes from Javier's mansion, and is found by the two agents in a church outside the village, she agrees into helping them find Javier. The trio later come across a dam and find Javier. After Leon and Krauser are swept away by a surging water current, they meet up with Manuela again and she reveals that she carries the T-Veronica virus. Leon and Krauser later infiltrate Javier's mansion and come across Hilda Hidalgo, who was Manuela's mother that had been infected and turned into a monster. She is killed by Leon and Krauser, but manages to infect Krauser with the T-veronica virus and Krauser is badly injured. Javier fuses with the T-veronica plant in the greenhouse and later becomes a dinosaur-like monster known as the V-Complex . When he attempts to kill Leon, Manuela reveals her powers with the Veronica virus and uses her blood to burn the mutated Javier. Eventually, the three manage to finally defeat Javier. Leon is able to save Manuela from losing too much blood and the three escape on a helicopter. Jack Krauser retires from the army and goes missing. He is later assumed dead in a helicopter crash. Albert Wesker watches over the battle and observes Krauser's abilities and determines he may be useful in the future.
- April 7
- April 9
- April 16
Another entry is made regarding the Torpedo Kids.
- May 18
- May 19
- May 20
Umbrella workers attempt to capture a "Glimmer," for research, but underestimate its strength. It manages to kill two people, then escapes.
- May 21
- May 22
Umbrella workers succeed in killing a Glimmer.
- June 1
- August 1
Albert Wesker, in B.O.W.-related business with Javier Hidalgo, advises him to "terminate all Russian routes" in the monetary transactions.
- August 7
Wesker informs Javier of an update to the "merchandise" list.
- August 13
Javier Hidalgo and his agent Sergio discuss their contract with Umbrella supplies - should they give in to a 50% increase in their purchases? Javier has Sergio check up on the broker raising the price.
- August 14
- Sergio obtains information from the broker - Umbrella was intentionally raising the price for profit, attempting to trick Javier into thinking that there was a lot of demand. Javier researches the man and discovers that he is an agent from Umbrella - he orders Sergio to eliminate him.
- Wesker 'confirms' that the Asian woman involved in the dealings is a spy for Umbrella, and that they should use "her".
- August 21
Wesker advises Javier to "be cautious" over the Asian broker.
- August 27
One of the freight crewmen on board the Spencer Rain writes his diary on the 100th day of him being on board.
- September 4
The Freight Crewman writes about cargo going into the ship's Presentation room.
- September 6
The Freight Crewman notices the biohazard symbol on some cargo.
- September 7
The Freight Crewman talks of his recent disciplinary.
- September 14
One of the waiters on board the Spencer Rain cruise liner writes a letter to his brother.
- September 16
The administrator of the cruise liner Spencer Rain notes some improvements that need to be made.
- September 18
Morpheus D. Duvall attacks the Umbrella lab in France that is still operational, he steals three t-Virus samples and loads them into missiles for terrorism purposes. The Paris Umbrella Laboratory sends a fax regarding the recent attack.
- September 20
A spokesman congratulates the captain of the Spencer Rain for four months of safe voyage.
- September 21
The Spencer Rain's captain becomes concerned that experimental bioweapons hidden in the ship's cargo have escaped.
- September 22
- Morpheus attacks and claims the Spencer Rain and spreads the t-Virus throughout the ship. He holds China and America at ransom otherwise he will launch the t-Virus missiles.
- The captain is the only survivor of the attack, and writes in his journal the futility of sending a distress call. He becomes a zombie soon after.
- September 23
A US-STRATCOM agent; Bruce McGivern, is sent to the Spencer Rain to halt Morpheus' Bio-terrorist threats. While encountering numerous BOWs, he also meets China agent Fongling and the two work together to stop Morpheus. Eventually, the runaway cruise liner is about to strike a cliffside and Bruce abandons ship moments before impact while Ling escaped via helicopter. Bruce later uncovers an abandoned disposal facility and discover's Morpheus's trail through a sewer system. After Bruce and Fongling make it past several unique BOWs such as the torpedo kids and glimmers, they enter the missile silo that Morpheus planned to use to attack USA and China. Bruce manages to defeat Morpheus after mutating into a Giant blob (contrary to his belief of beauty) and destroys the missile silo from his explosion minutes before missile launch. Bruce and Fongling are eventually rescued from a chopper as Fongling tells Bruce she belongs in China despite Bruce wanting her to come to the US. 
- Resident Evil: Dead Aim, Biological Report 1
- Resident Evil: Dead Aim, Biological Report 2
- Resident Evil: Dead Aim, Ship's Log
- Resident Evil: Darkside Chronicles, Communications from Wesker (Faxed Documents)
- Resident Evil: The Darkside Chronicles, Javier's Private Messages
- Resident Evil: Dead Aim, Freight Crewman's Diary
- Resident Evil: Dead Aim, Waiter's Letter
- Resident Evil: Dead Aim, Admin Report
- Resident Evil: Dead Aim, Emergency FAX from Paris Branch
- Resident Evil: Dead Aim