Makoto Ishki is a mass produced clone, codenamed "Type D." What separates Makoto from the rest though, is that he was raised along with two potential instrumentalists --Itsuki and Helena, and thusly recieved special education and training. When he was just a child, he discovers how Bahbem produces clones when he finds a living rock at the bottom of the mansion; this rock was a failed Dolem during its early stages. He takes affection to this rock and keeps it as a pet. But through his discoveries with this rock, Makoto realizes that he might be just another clone and starts to think about the existence of his parents. Feeling like he's nothing but an expendible tool, He tries to escape the mansion along with this rock but it all collapses the moment it leaves the mansion.
Ever since then, Makoto developed a severe identity complex, he especially cannot stand anybody who calls him a "D" since it would infer that he's nothing but a mass produced product. He then sets a life goal that he will out-do any D-clone and stand out purely because of his deeds, not because of his genetic make up. However, he can be a bit too manipulative and he's somewhat of a dick, so he earns his little nickname around Terra as the "white snake" (because he always dresses in white).
Towards the end of the series when Kunugi is fired because Ayato escaped with the RahXephon and Quon, Makoto then succeeds the position of commander. He then proceeds to start "Operation Downfall" with the goal of bringind down the Tokyo Jupiter barrier. He succeeds, but after a brief moment of victory, it all comes crashing down when more Mulian cities started appearing out of nowhere, making his operation a complete failure. This is also due to Mishima controlling his mind and taking whatever steps she instructed him to do. Because of his he's incarcerated and completely loses his sanity. Between all the turmoil at the end of the series he finds a way out and starts a killing spree of D-clones. He makes his way to Bahbem and attempts to kill him, however he is killed by Bahbem's helper (the girl with the tan) when shot in the head.
Makoto's only friend was Itsuki.