Alexander took over the development of the Little Sisters and Big Daddies following the untimely death of Yi Suchong. In particular, he was responsible for developing the bond between Eleanor Lamb and the game's protagonist Subject Delta. He also developed many of the Security Bots and other defense mechanisms encountered across Rapture. Over time, he became invested in Lamb's notion of the "Utopian" and ultimately volunteered himself for the project. Sadly, the ingestion of ADAM and the experimentation left Alexander as a twisted fetus-like monstrosity within a tank. Adding to the sadness was his abandonment by Lamb, whom Alexander admired and very likely had feelings for. This surely made Alexander all the more insane in his seperation.
Prior to this, he anticipated losing his sanity and left a set of Audio Diaries and procedures for anyone to confront him. These become crucial to the level.
As Subject Delta arrives in Fontaine Futuristics, he is accosted by a Security Bot wielding the image of human eyes. They belong to "Alex the Great", the post-mutated form of Alexander who spends his time torturing the Splicers trapped in his employ. Subject Delta tries to follow pre-mutation Alexander's procedures, but is initially cut off from accessing his tank by Alex the Great's Security Bot. He also launches failed Alpha Series Big Daddies to attack Delta in the process.
Delta is then forced to destroy Alexander's control over the Security Bots in order to access the inner chamber. Therein, Delta retrieves a DNA sample from Alexander in his tank and gains access to Perspehone as a result. In his final Audio Diary, pre-mutation Alexander urges the listener to euthanize him via an electrocution function of the tank while Alex the Great pleads for his life. Delta is given the choice to kill or permit him to live. His choice is reflected later in the Little Sister section where a statue portrays Delta as either rescuing a man from within the beast or simply combatting it. If spared, it is unknown what becomes of him.