- A bee crashes into the Voot Cruiser and causes it to crash-land. Zim nicknames it the "Death Bee". Later, the same bee crashes into the Voot Cruiser Recovery Vehicle, causing it to make a crash landing as well.
- Zim thinks that Tak is after his Robot Bee and holds it out. After Tak leaves, the robot bee flies away.
- In this unfinished episode, Zim would have volunteered at the "Bee a good neighbor" program and worn a bee suit. Dib would have also volunteered at the program to follow Zim and worn the same bee suit uniform.
- This unmade conceptual episode would have dealt with Zim having to eliminate a hive of meat-obsessed bees that have infested his base.
- The Kyle Starks variant cover features Zim being surrounded by bees.
- When Zim orders the disguised Dib to clean out the honey-coated puppies GIR keeps in his head, he warns him that the honey has attracted bees. A swarm of them then come out and sting Dib.
- In the backup comic "Keep It To Yourself", GIR is eating honey, which would appear to be full of bees, as a swarm of them come bursting out of his head, and begin stinging Zim.
- Zim mentions that he's taping bees together as part of a plan. An explanation on why is not given.
- At the end of the Issue, when the Robo-Hobo finishes telling his story about Zim and Li'l Meat Man, one of the containment boxes next to his contains what appears to be a large bee, possibly the Robot Bee.
- At one point during Dib and his father's argument about Dib's paranormal studies, mention is made of a vampire bee that Dib claims stung him, causing him to eat lots of honey. After their argument is over, a bee with fangs and wearing a cape is shown sitting on a nearby bottle.
- During the climactic chase scene between Dib and Zim, the former encounters sentient Alien Bees on one of the planets being sucked into the Florpus Hole. Dib flies one of them as he attempts to take Minimoose away from Zim in order to save the Earth from the Irken Armada and the Florpus.
- Dib mentions the vampire bee among the various things that he'd rather be investigating than focusing on stopping Zim's plans.
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