In this episode, it is revealed that Fry's cryogenic freezing and arrival in the 31st century was not an accident, but a calculated plot by Nibbler to save the universe.
The Nibblonians explain that because Fry lacks the delta brainwave on account of his being his own grandfather, he was immune to the attack of the Brain spawn a few months prior.
The Nibblonians give Fry a "Quantum Interphase Bomb" which will send the sphere into an alternate dimension forever, as well as a wind-up toy vessel with which to reach and escape the Infosphere.
In the alternate dimension, the Brain spawn offer to send Fry back in time to stop Nibbler from freezing him.
Jokes about the extreme mass of Nibbler's feces and mention of Vergon 6 call back to "Love's Labours Lost in Space".
[1] The planet Eternium, the Brainspawn, and the delta brainwave concept were originally introduced in "The Day the Earth Stood Stupid".
[1] Cohen also notes that in the episode "Jurassic Bark", a shot of Nibbler's third eye sticking out of a trash can is included as a reference to these events as well, an item which many fans had noticed.
[1] Creator Matt Groening also notes that they had planned to hold off on using time travel plot lines until the series was better established.
[2] Cohen jokes that perhaps they should have explored this plot point earlier however since at the time the episode commentary was recorded it had become clear that the series would be ending.