The second stage describes a growth alteration which occurs when SCP-003 comes into contact with living organic material; SCP-003 appears to "template" itself off of the organic material, and will attempt communication with organisms that match its initial "template" or "templates".

In its second stage, SCP-003-1 may pause, slow or change its growth, and will also convert inorganic and nonliving organic elements into functionally similar structures while anomalously altering their physical makeup.

While growth is consistent in the first stage, in the second stage SCP-003-1's growth rate is diminished by 20-90% so long as SCP-003-1 remains in contact with living organic material. The percentage is determined by the complexity of the organism(s) in contact with SCP-003-1; SCP-003-1 appears to devote a large amount of processing power to analysis of living organic material.

During each of SCP-003-1's growth stages, SCP-003-2 releases bursts of radiation that temporarily inhibit SCP-003-1's growth, or reverse this growth when the temperature of SCP-003-1 rises above 100°C. Similar radiation emissions have been replicated or recorded via other anomalous means.