Eventually, Zim manages to destroy Earth, leaving it in ruins. He then returns to Irk, but he forgets GIR who was playing around with some pig-related things, leaving GIR stuck on Earth.
Over the next 700 years, GIR lives his life on Earth, playing around in the ruins with Mini Moose. He lives in the house that was once his master's base. He keeps his circuitry stable my collecting and harvesting electronics from the human stores He watches movies, plays video games, and reads pre-schooler books to pass the time. He collects many other interesting items and knick-knacks. After some time, GIR becomes very lonely.
One day, after the 700 years, GIR finds a plant growing in the ruins, and takes it home and puts it into a coffee cup as a pot. Later, a ship that is seemingly Irkan lands near his location, and deploys a SIR unit who looks awfully familiar, and beautiful. GIR soon recognizes the SIR as Mimi, Tak's SIR. While GIR is in love with MiMi attacks anything that moves at first, even GIR and Mini Moose, but soon realizes neither of them pose a threat (even thinks Mini Moose is cute). She seems to be scanning the area for some unknown objective. When a sandstorm starts, GIR takes MiMi to his base for shelter, where he shows her his collection, but when he shows her the plant, she stores it in her head and goes into stand-by mode.
While she is in stand-by, GIR takes her outside, thinking her solar battery needs recharging, works hard to protect her from the rain and snow and strong winds. He later takes her out on a "date". Eventually, the Irkan ship that dropped MiMi off comes to pick her up, and GIR manages to hitch onto it to follow her. The ship takes them (and other SIR units that have been scouting other planets) to a huge Irkan ship that somewhat reminds GIR of the Massive.
The sanitizer SIRs, the lead of which includes Chipz, the SIR unit that was once Skoodge's unnamed SIR unit comes to clean up the SIR probes. When Chipz gets to GIR, however, he starts obsessivly trying to clean him up. Guard-84, robotic head of security inspects the probing SIRs, and when he comes to MiMi carrying the plant, he has her sent up to the bridge for the Tallest to see, and GIR follows them. While following them, GIR sees all the Irkan people lying around in hover chairs being lazy, and robots doing all the work for them. When they get to the bridge, they meet AVI-8-Tor, called "Ator" by the Tallest later, the auto-pilot of the ship.
The new Tallest is sent up (He is not Red or Purple, as everyone in Zim's generation is long dead by now), and begins inspecting MiMi and hearing video logs and instructions left by Tallest Red years ago. It becomes clear here that MiMi was sent to see if Earth can sustain life to see if the Irkans can go live there as their homeworld. It is also revealed that all planets that were formally owned by the Irkan empire have become unable to support life for whatever reason.
When the Tallest opens MiMi's storage head, however, the plant is missing, and Tallest considers her broken, and has her sent to the repair wing. He also meets GIR, and after seeing how dirty he is, orders him down to the wing as well to be cleaned. MiMi blames GIR for the plant missing and avoids him. During MiMi's check up, GIR thinks she is in danger, and destroys the wing (mostly by accident), and makes both him and MiMi wanted targets of the security, thus igniting her anger at him further.
MiMi attempts to get GIR back to Earth via an escape pod, but he refuses to leave without her. Soon, Guard-84 comes, and sends the plant out in an escape pod, programming it to blow up, but GIR manages to save it, and a happy MiMi gives him a robotic "kiss" and dances with him around the Massive before returning to the inside so MiMi can give the plant to the Tallest. GIR waits out by the pool while MiMi goes up the garbage chute to the bridge.
Upon arriving on the bridge and giving the plant to the Tallest, the Tallest then figures out how to use it to bring the ship to Earth so the Irkan race can live there. He has MiMi's camera recordings played so he can see what Earth looks like, and sees how destroyed and run-down it is. Also during this time, MiMi sees how GIR was caring for her while she was on Stand-by, and falls in love with him in return.
Meanwhile, GIR is growing tired of waiting for MiMi, and climbs up the garbage shoot after her, with Skoodge's SIR right behind him and cleaning up his tracks. On the bridge, the Tallest tries to tell AVI-8-Tor to set the Massive's coordinates for Earth, but 8-Tor, who has been given orders from Tallest Purple (who prefer's the Massive's lazy and luxurious life) years ago, stages a mutiny with the security, and attempts to throw the plant down the garbage shoot, but it is caught by GIR. Guard-84 uses telekinesis to grip hold of MiMi, while 8-Tor electrocutes GIR with a lightsaber-like handle. Both SIRs are then dumped down the garbage chute with the plant, and the Tallest locked in his quarters.
In the garbage disposal room, MiMi comes to her senses while a badly injured GIR is about to be sent out the airlock. With the help of Chipz, MiMi manages to save him and herself. MiMi frantically searches for a new drive to replace GIR's damaged one, but to no avail. Chipz cleans up GIR finally, then relaxes. GIR hands the plant over to MiMi so she can carry on her mission, but she does not care about the mission anymore; she just wants GIR to be okay. GIR then reminds her that he has spare parts back on Earth in his base, and so MiMi carries him and Chipz out of the garbage room and into the hallways.
The Tallest manages to make an announcement instructing MiMi and GIR to bring the plant to the main deck to place the plant into the ship's holo detector and the ship can lock onto Earth and jump there. (The Tallest also comments on that being a stupid design for the ship, having the holo detector on the deck rather than the bridge.) GIR and MiMi, with the help of Chipz and the other SIR units, manage to break through 8-Tor's security and get to the deck. Meanwhile, the Tallest battles 8-Tor and activates the holo detector and the ship goes into lockdown mode, and drags out all passengers onto the deck. Right before the situation gets critical, 8-Tor knocks down the Tallest, and tilts the ship, causing all passengers to slide out of their chairs, and GIR to drop the plant. While MiMi searches for the plant and protects the passengers from a falling hover-train, 8-Tor tries to close the holo dtector. GIR tries to hold it open with his own body, but soon gets crushed when 8-Tor pushes down on it, much to MiMi's horror. Right then, the Tallest stands up, shuts down 8-Tor, and levels out the ship. The Irkans, and the other robots all toss around the plant until it is passed to MiMi, who pushes open the holo detector and tosses in the plant. The Ship then jumps through hyper space until it reaches Earth.
Upon landing on Earth, MiMi takes GIR's crushed body to the base, and quickly makes repairs. Upon finishing, however, GIR seems to be just a regular SIR unit, devoid of emotions, and does not remember any of his adventures. MiMi tries to restore his memory with Mini Moose, piggies, food, the scary monkey show, and pictures of him and Zim, but nothing seems to work. GIR walks outside and starts blowing up structures and cataloging notes like a normal SIR unit would do, leaving MiMi to believe the GIR she knew and loved is gone forever. Heartbroken, she slips her hand into his, and gives him a final farewell "kiss". The spark reboots his memory, however, and the two are happily reunited. The Irkans begin to settle in their new home, and restoring the planet's biosphere with the help of the robots as GIR and MiMi live happily ever after.