The Fourth Doctor and K9 Mark II spent an indeterminate period of time together. However, the Doctor appeared to be activating K9 Mark II, implying that no significant time had elapsed since leaving Gallifrey. (TV: The Ribos Operation) It is possible that the Doctor spent some time at Nest Cottage before activating him. (AUDIO: The Stuff of Nightmares)
After K9 Mark I regenerated into K9 Mark 2, his design was radically altered. His ear probes were replaced with larger silver aerials. A set of blue lights on his head flashed when he spoke. Most of his body was dark silver and a silver dog bone was located under his neck. He seemed to have the same capabilities as Mark I but was presumably more advanced. (TV: Regeneration)
Jealous, Possessive by Paul Magrs, the "Scorpio" story in Big Finish's anthology Short Trips: Zodiac features K9 Mark I and Mark II relaying their exploits to each other, and their veiled put-downs to each other reveal that each considers the other to be the "inferior" version. This attitude is also occasionally hinted at in the way the two units refer to each other in the Gallifrey audio series.
During Romana's Presidency of Gallifrey, Leela became her bodyguard, and the two K9 units were forced to work together, not always amicably. After Matthias had replaced Romana as President, he nominated her to undertake a mission to find a cure for the Free Time virus, to be followed by exile. K9 opted to remain in the employ of Matthias, fighting the infection on Gallifrey. However, Braxiatel and K9 had planned another operation. Realising that the only cure to the virus was to end the regeneration capabilities of the Time Lords, Braxiatel used a Time Scoop to collect the Time Lord bio-data archive (along with K9). Romana was asked to decide whether to administer the cure or let Gallifrey die and rebuild it from scratch with the bio-data archive. (AUDIO: Gallifrey)
K9's innards were redesigned twice more over the course of the series, firstly in collaboration with a company called Slough Radio Control. It allowed one of its employees, Nigel Brackley, to be seconded to the series semi-permanently to supervise the prop. Brackley, who has since gone on to a career in the movie industry, controlled K9 for many of its studio appearances. Eventually, there came a point where the dog's inherent liabilities were outweighing his assets, and the internal mechanisms were completely rebuilt by designer Charlie Lumm. The wheels were enlarged and given independent drives for power and better manoeuvrability, and the radio controls were switched from AM to FM signals to resist interference. However, by the time the improved model made his debut in State of Decay, the first story recorded for Season 18, the decision had already been made to write the character out of the series in the adventure Warriors' Gate.
K9 Mark III first appeared in "A Girl's Best Friend", the 1981 pilot for a series, K-9 and Company, which never materialized beyond the first episode. In this, the character is presented to the Doctor's former companion Sarah Jane Smith (Elisabeth Sladen); together, the two embark on what a number of adventures. Only the first of these is depicted on-screen; several are shown in comic book and audio play adaptations, and others are alluded to by the television series. Mark III made a brief appearance alongside Sarah Jane in the Doctor Who 20th anniversary ninety-minute special The Five Doctors (1983), before appearing properly and for the final time in the revived series' episode "School Reunion" in 2006. By the time of that story, Mark III has fallen into disrepair and eventually sacrifices himself to stop a plot by the alien Krillitane and defeat their leader, Lucas Finch (Anthony Head). In the episode's conclusion, the Doctor presents Sarah Jane with a new K9 to encourage her to continue investigating alien activity; the Doctor "rebuilt" him after the Mark III's sacrifice, implying that he had the same mind and memories as his predecessor while still being a "brand new model".