When Zygote transforms into the Lemurian-like creature, the wires that connect him to the machine disappear, seemingly turning into a mustache. They are not seen for the rest of the transformation, even when he turns into a pure thought. Though before the final evolution, Zygote again pulls those wires out of the machine.
In the end, Zygote is pure thought. He has immense abilities and has evolved beyond the infinite... Yet for some reason, when he wants to get out, he has to open a window. How could the glass hinder him in that state?
Max: You're out of your mind, Eggbert! And you're out of mine!
The episode resembles closely Edmond Hamilton's story "The Man Who Evolved", in which a scientist invents a machine which accelerates evolution, and goes through the different stages of the human development.
Also, in the story, when the scientist, on a certain stage, expresses a desire to rule the humanity, he is stopped in a similar way to the cartoon, meaning, convinced to continue his evolution. On the next stage, he is beyond such desires.
Virgil's means of summoning: Out of Max's many baseball cards, he finds cards for Virgil and Norman. A message is placed in one of the cards. The message was "Portal at 723 Murietta Street."
Educational Epilogue: Genetics (DNA and cloning)
During the sequence where Zygote evolves himself, he briefly turns into a Lemurian (a bird-like humanoid, like Virgil). This bit was edited out in syndication for some reason.