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Wesker does not make direct contact with the Redfield or Ashford siblings throughout the scenario; however, his voice can be heard when Steve and Claire make their way from the island palace to Alfred's private residence (with Claire apparently sensing his presence) and is in full view at the end of the scenario's final chapter. In addition, Chris only seems to deduce Wesker's survival when he sees his knife near a carved message on the pillar.
Alexia kills Alfred herself for not waking her up on time, rather than mourn his death as she did in the original game. By consequence, Alexia's reason for capturing Claire and Steve and experimenting on the latter was just for the sake of it rather than as revenge for their role in Alfred's death as was the case originally.
Chris meets Steve.
Claire helps Chris fight Alexia.
Wesker does not fight Alexia.
Alexia speaks when mutated.
On a related note, all of Alexia's forms are fought in the same area, which was originally where her second and third forms were fought. In addition, although she implies that she did get injured when her first form is defeated, it was apparently less severe than it was originally.
On top of this, Alexia's transformations were altered, depicting the Alexia-Pod's assisting her with additional bio-mass for her second mutation.
Chris and Wesker did not fight in the final battle at Antarctica, as they did in Code Veronica X.
