It is first heard when her ship's computer informs Samus about the SA-X when she enters Sector 2, and warns her to avoid the creature. When Samus enters the breeding tank where Serris was kept in Sector 4, this theme will again play, and continue into the shaft before the room in which she fights Serris. It plays again in Sector 5 in the room where the SA-X is encountered, but stops playing as soon as Samus walks into the room far enough to trigger the SA-X's entry. Disquieting is later heard on the first visit to the vegetation-infested Reactor Silo, and continues until Samus reaches the room where she battles Yakuza.
Next, it is heard when Adam reports that he has sighted the Security Robot B.O.X. in Sector 6, and when Samus discovers the Restricted Laboratory. The final time it is heard is, when it learns about the original Adam, the computer asks Samus what he would do about the X Parasite and SA-X. It continues until the computer regains its original personality as Adam, and he suggests that Samus crash the station into SR388.
The theme can be heard here.