The Biological CPU was a secret Atlantic Federation and Eurasian federation development project, aimed to produce pilots for its mobile suits that would fight with the same efficiency as Coordinators. In its earlier stages, the project was codenamed Biological CPU program.
The Biological CPUs were thought to actually have their brains replaced with CPUs. Hence the name "biological CPU". The brains seen at the Lodonia facility in Gundam Seed Destiny prove this.
- First Stage Biological CPUs had some biotechnological modification and were mentally conditioned to eliminate their sense of fear and increase aggression in combat; the subjects were mostly regular pilots who were given regular doses of the performance-enhancing drug Gamma Glipheptin. This drug had a negative effect on the pilots' mental stability and caused them to behave in undesirable ways during battle. It also had very brief duration, and as the effect wore off it left the pilots incapacitated with severe withdrawal symptoms, as their nervous systems began to collapse without regular doses. Their loyalty to the Alliance was guaranteed by their addiction to Gamma Glipheptin. The first-stage test subjects were Clotho Buer, Orga Sabnak and Shani Andras, . All three were killed in battle during the closing stages of the Bloody Valentine War. Due to their required intake of drugs and harsh withdrawal symptoms, fans dubbed the trio "the Druggies", which tends to be used as an affectionate nickname rather than an insult.
- Second Stage Biological CPUs were physically and psychologically altered with brainwashing, heavy mental conditioning, performance-enhancing drugs and extremely harsh combat training. They were more stable than first-stage Biological CPUs, but required regular re-conditioning, especially when their trigger words were used to force actions from them. They also required regular brain "maintenance" to keep them in a high-performance state, and to erase any "undesirable" memories they might have. Sting Oakley, Stella Loussier, and Auel Neider were second-stage Extended humans. All three died in combat. Auel perished at the hands of Shinn Asuka's ZGMF-X56S Impulse in a naval battle near Crete. Stella died after her GFAS-X1 Destroy was attacked by Kira Yamato's ZGMF-X10A Freedom in battle over Berlin. Sting was killed by Shinn's ZGMF-X42S Destiny in the battle for Heaven's Base.
First Stage Biological CPUs possessed strong enough combat abilities to press even very strong Coordinators such as Kira Yamato or Athrun Zala. However, Second Stage Extended humans proved to be somewhat weaker than their predecessors. Evidence of this is the fact that they could not hold their own against characters in SEED mode while the original Biological CPU pilots did.
Biological CPUs could be considered analogous to the Universal Century concept of Artificial or Cyber-Newtypes, who were normal pilots enhanced to have Newtype abilities.
- The methods used to train and enhance the Second Stage Biological CPUs are similar to the SPARTAN-II Program from the video game series Halo.