The chapter begins with Gina and Colette arriving at the Anomalous Materials department right on time, in contrast to Gordon being late in Half-Life. They are greeted by a security guard, who comments on how today is "the big day" and they will be working with the "new guy, Dr. Freeman". He also explains that a recent system crash may have wiped them from the security system, so they'll have to sign back in in the next room. After getting scanned and re-added to the security system, the two Doctors head to the Anomalous Materials control room. Dr. Keller greets them but shows his annoyance at Freeman's lateness, saying "[he does] not understand what Kleiner sees in that boy". Dr. Rosenberg then enters the control room and displays his disapproval at the Anti-Mass Spectrometer being pushed to such a high power capacity for the analysis. However, he caves in after Dr. Keller says it is not his decision and if he doesn't wish to see the experiment he can go back to "[his] little labs over by the train yard".

Cross and Green go down to their respective areas for the experiment. Gina goes to the delivery chute to push the sample up to Gordon, and Colette goes into the lower area of the test chamber to turn on the power and set it to 80%. After Gina fixes a small problem in which a crowbar was mysteriously jammed inside the delivery chute's mechanism, the sample is moved up to Freeman and the Resonance Cascade occurs. Cross and Green black out for a period of time, and wake up to see the lower part of the test chamber in shambles. They hear Dr. Keller and Rosenberg over the intercom, who discuss what to do. Dr. Rosenberg is intent on saving the personnel in the facility, while Dr. Keller wants to fix the tear created by the resonance cascade, saying they caused this mess and should be responsible for fixing it.

After finding pistols and fighting their way through part of the laboratory, the two doctors make their way back to the control room. Keller and Rosenberg tell them they have reached an agreement. They will escort Dr. Rosenberg up to the surface to call the military, and Keller will stay below to assess the damage made to the equipment. With any luck, he'll be able to find what caused the experiment to go wrong and how they can put things right. Dr. Cross, Green and Rosenberg enter the elevator to get to the surface through the Hazard Course, and the mission ends.