-Holly (RD: Nanarchy)
The nanobots' job inside Kryten was to make sure that all his systems were operational. As nanobots are subatomic they can change anything's component atoms into any other thing - such as turning a pencil's carbon arrangement into a diamond's carbon arrangement - a useful tool for repair.
According to Kristine Kochanski, nanobots are the same in her dimension. After they deserted Kryten, it was Kochanski who suggested looking for them to rebuild Dave Lister a new arm. The search lead to the discovery of what had occurred with their mothership Red Dwarf, and ended with Red Dwarf being reconstructed and upgraded, and the original crew (who had been reduced to piles of dust due to the radiation leak in the pilot episode) were also resurrected by the nanobots.
Over the past three million years living inside Kryten, the artificial intelligence of the nanos had evolved, and they had started to have ideas of self-determination, much as their mechanoid master had,The nanos eventually got bored of living inside the mechanoid and escaped from Kryten while he and the rest of the Red Dwarf gang were exploring the ocean moon where the SSS Esperanto was found ("Back to Reality", Series V). The nanobots then escaped in a tiny version of Red Dwarf they created leaving the crew stranded in Starbug, and Holly trapped on the planet they made out of the excess material from the large Red Dwarf.
Two series later, the gang believed to have found them again in "Nanarchy", the final episode of Series VII. They were able to communicate with them through the Universal Translator. Kryten trapped them in a glass jar out of Lister's laundry basket, and forced them to obey his commands again, ordering the nanos to rebuild Red Dwarf (and give Lister a new arm which he lost during "Epideme"), which the nanos do, but also giving him the body of a steroid user, even upgrading Red Dwarf to it's original 'intended' state before the JMC made 'cut-backs'. This included bio-organic ship-wide networking, a new antimatter reactor, and a Karaoke Bar on C Deck. However they initially turned the ship unfathomably massive, so the Starbug was tiny enough to fly up a rat's rectum. The ship soon stabilised to its normal size.
It was Holly, whom they found on the Red Dwarf planet (now back in his male form), who was the one to figure out where the nanobots were. The nanobots also resurrected the original Red Dwarf crew (who had all been turned into piles of dust by the radiation leak in the pilot episode), which would soon lead to the old Red Dwarf crew being arrested for stealing and destroying Starbug.
To try and show their resurrected captain the truth the Starbug crew tried to prove their wild tale of the accident, nanobots, and three million years by trying to find the nanobots, but the nanobots had fled the ship after recreating it.
In the end they were kept in computer simulation and did prove their story accidentally while in there, before being arrested for the fraud they tried to use earlier to escape - using the confidential crew files in the crashed Starbug from the older version Red Dwarf. Holly then admitted that he in fact had created the new set of nanobots and told them to recreate the ship and resurrect the crew, to give Lister a diversion to keep him occupied and sane. Holly than commented that his plans had "all gone tits up", and the regular characters are taken to The Tank. (Back in the Red)
- The Inquisitor was a self-repairing Simulant who survived until the end of time before building the Time Gauntlet. He is seen rapidly "regrowing" his hand, presumably through nanotechnology, after having his hand cut off by Kryten using a holo-saw in the Series V episode of the same name.
- The old pre-scientific alchemists of Earth had attempted to rise the dead from their cremated ashes in a process known as Palingenesis. Of course, it never worked, but this is ironically exactly what the nanobots achieved - resurrecting the old crew of Red Dwarf from the piles of irradiated ashes that were left of them.
- The nanobots should not have been able to resurrect the old crew of Red Dwarf, since after the accident, Lister had shot off their ashes into space inside canisters. If the ashes were no longer on board, then the nanobots should not have been able to use the ashes to "rebuild" their bodies and restore them to their previous state. However, this does not necessarily affect continuity, since the funeral Lister held for the crew is of uncertain 'canon'. The funeral scene was never broadcast, instead being a deleted scene for the pilot episode included on the Series I DVD.
- The ultimate fate of the nanobots is unknown, since after recreating Red Dwarf and resurrecting the old crew in "Back in the Red", the nanobots flee the area, never to be seen again.
Behind the scenes
The nanobots were essentially the antagonists and a MacGuffin for Series VI - VIII, the cause of all that occurred, with them stealing Red Dwarf, leading the Dwarfers on a merry chase around the Galaxy on Starbug, and resurrecting the ship and original crew, landing the Dwarfers in The Tank. Their invisible nature and effectively boundless power make them at once a MacGuffin and a supervillain.