You probably noticed that the lip movements don't seem to match
the dialog in this episode, and that some bits of animation were
used twice. What's the deal? Well, the script was written
to use animation from an existing production. The entire
recording was an ADR session.
The animation came from an episode that was to serve as a
pilot for Zalgar the Brain Eater, much how Mork
appeared in Happy Days before having his own show.
In the episode, the first brain that Zalgar goes after is,
of course, that of The Brain.
The writers were given the task of taking animation from the
Zalgar-centered story and somehow reworking it so it became a
story centered on Pinky and The Brain, and trying to match
syllables in their new script with the number of lip flaps
in the animation they wanted to use for each line. None of
the credited writers was the writer of the Zalgar story, so
I don't think any existing lines from that pilot were left
intact.
According to one source, a line from the original script was:
BRAIN
This is where the government keeps everything they don't
want you to see.
PINKY
You mean like Ernest Borgnine from underneath?