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Professor Clay was seen when he tortured Hydranoid into creating Hades (Hydranoid's mechanical counterpart) by using Hydranoid's DNA for Shadow Prove.
It is unknown if it's possible, but it's confirmed that Professor Clay was responsable for turning his son Keith into a Vexos member called Spectra Phantom.
Professor Clay created Altair, a Mechanical Bakugan for Lync Volan in Cyber Nightmare, he used his evil plan to create the Mechanical Bakugan for the Vexos.
In the episode 52, he saw a video from Fabia about the Gundalian Bakugans, when the Alternate Weapon System was destroyed, King Zenoheld and Prince Hydron died, it is unknown if Professor Clay has survived in the destruction of the Alternate Weapon System.