Resistance: Fall of Man
Dr. Malikov doesn't actually appear physically in Resistance: Fall of Man, but he does appear in photographic form. When Cloven commited suicide, they often placed a picture of their leader inside their mouths. This picture was of Dr. Malikov, who created the Cloven while experimenting with the Chimeran virus in Russia.
Following their creation, the Cloven became his personal bodyguards and were neither friend nor foe to either the Chimera, or Humans. However, they did enjoy watching them kill each other.
Malikov appears towards the start of Resistance 2, and he is now assisting SRPA. He initially performs an operation on Nathan Nale after he is taken to San Francisco and informs Nathan that he must receive his inhibitor treatments to try and contain the Chimeran virus inside him.
After the San Francisco disaster, Malikov decides to head back to a research facility in Bryce Canyon in Utah which he managed to take control of. He went to try and find a way to stop Daedalus but when he was there, he realised he was too late.
I Created All Of This
While in Bryce Canyon, Malikov reveals that the recent resurgence of Chimeran activity is his fault. He injected pure Chimeran DNA into both Nathan Hale and Jordan Shepherd. While Hale managed to retain his humanity, Shepherd wasn't so fortunate and turned into Daedalus.
Daedalus let's Malikov live when they meet in Bryce Canyon, and Malikov presumes this is so that he can bear witness to the Chimeran resurrection. With Hale's help, they are able to defeat the Swarm and leave Bryce Canyon.
It May Be Our Only Chance
Shortly after his rescue from Bryce Canyon, Malikov hatches a plan which he hopes will destroy the Chimeran fleet. They appear to be gathering above the Chicxulub crater in Mexico and his plan is to use a fission bomb which should hopefully start a chain reaction and wipe out the fleet.
After sending his memo to Major Richard Blake, it is presumed that Malikov committed suicide. He makes a diary entry where he talks about overdosing on morphine and he apologies for what he has caused.