so let me clear you from start
crySis 1(2020): during the incident of Lingsham island his suit started to merge with prophet's mind later when things went FUBAR and he was MIA he did Something and got access to alien technology Thats Why he knew so much about the Cephs.
Later he upgraded his suit in USS CONSTITUTION
2.CRYSIS COMIC (2020-2023):
HIS SUIT WAS STILL MERGING WITH HIS BRAIN DOWNLOADING MEMORIES OF PROPHET , you can say making a backup!
Soon when he discovers of Cephs in new York city he tries to warn the authorities But he was late ,
3.crySis 2:(2023) -
with the city infected by deadly alien Manhattan virus . Prophet was infected too may be because he was in the ship of Ceph in his attempts to Find the alpha Ceph.
As soon as he discover he's infected and has no choice other than passing his work to other person prophet finds Alcatraz HALF DEAD. he tried to suicide Which failed.
Actually he was able to kill the virus infected body But not his brain and memories Which the nanosuit 2.0 stored as backup.
As Alcatraz the bearer of N2 with serious internal damage the N2 keeps him alive by taking over his body's functions like controlled breathing , and function of heart etc. And on Same the suit is installing prophet's memories in Alcatraz's brain.
So its like parasite and host relationship.
At the End of C2 you hear something from your suit as "xx process complete"
that signifies that the merging of the suit and downloading of prophet's memories with Alcatraz's body and brain is complete.
And the voice is generated by suits inbuilt microphone.
So in C3 its like AlcaProphet
But in the End of C3 the suit fixes Alcatraz's body and reshapes it into prophet's.
Hope you got it