There are a lot of great 4th Doctor stories, particularly in the early days of the Tom Baker era when the great Phillip Hinchcliffe (producer) and Robert Holmes (Script Editor and chief writer) were in charge.
I think I've mentioned before that seres 13 of Doctor Who didn't have a single below-par story and every one was a classic. The very best 4th Doctor story (and a definite contender for the best ever), however, came in Tom Baker's very first series as the Doctor - series 12. The all-time classic "Genesis of the Daleks".
"Genesis of the Daleks" is third on my list of all-time favourites behind "The Dalek Invasion of Earth" and "The Web of Fear", but I must admit that is probably due to personal nostalgia for those two stories. "Genesis of the Daleks" was quite possibly the best Doctor Who story ever written. The acting was superb from all concerned, and it certainly had higher production values than any other story right up until Doctor Who ended it's original run in 1989. It also has been consistantly voted the best ever Doctor Who story in fan circles (in fanzines, on-line, e.t.c) ever since it was first shown on BBC1 in 1975.
The story of "Genesis of the Daleks" followed on directly from "The Sontaran Experiment", at the end of which the Doctor, Sarah Jane and Harry attempted to return to Space Station Nerva (where they had left the Tardis) by transmat beam.
The Time Lords, however, intercepted the transmat beam and transported the Doctor and his companions to Skaro instead, where they asked the Doctor to undertake a mission for them. I.e. to prevent the Daleks from ever being created. Russel. T Davies, in fact, cites this mission as the root cause of the later Time War between the Time Lords and the Daleks.
The Doctor is at first reluctant to do the Time Lords dirty work for them, but agrees when he finds out what the mission is. The Time Lord who met the Doctor on Skaro gave him a time ring, which would take him and his companions back to space station Nerva to find the Tardis when the mission was complete.
The Doctor and his companions, find themselves in the ruined and war-torn landscape of the planet Skaro, where the Kaleds and the Thals have been at war for thousands of years. At this point, their situation has become so desperate that they have reverted to using primitive projectile weapons, explosives, gas, e.t.c, rather than more high tech weapons. It turns out, however, that both the Kaleds and the Thals are involved in construction "ultimate weapons" which they think will wipe the other side out. The Thals are building a gigantic rocket which they believe can penetrate the Thal dome. Meanwhile, the Kaled scientific corps, under the guidance of their deformed chief scientist Davros, are developing something much more terrifying.
Davros, realised that contamination from the nuclear and biological weapons used in the war was mutating the Kaled race, and artificially accelerated the process to create the ultimate evolutionary end product and ensure the Kaleds survival. In the process, however, unknown to the rest of the corps, he removed what he thought of as "negative emotions" from the mutants (compassion, mercy, kindness, e.t.c), as part of his secret plan to create a life form capable of wiping out all other forms of life. A life form, which he would later name Daleks.
From there, the story involves the Doctor and Harry trying to convince various members of the Kaled scientific elite to assist them against Davros, and Sarah Jane's attempted escape and recapture from the Thal dome with fellow prisoners, but she is eventually rescued by the Doctor and Harry, after they are helped to escape from the Kaled dome by members of the scientific corps that they have convinced to help them.
In the meantime it becomes clear that there is increasing dissent among the scientific corps against Davros, and only his ruthless security officer Nyder, remains loyal. When the Kaled government then calls a halt to Davros's experiments, he decides to take action against both the Thals and his own people. He decides that his Daleks are now ready to take over, and plans to wipe out the entire Kaled and Thal population of Skaro.
In the Thal dome, the Doctor overhears Davros and Nyder having a meeting with the Thal leaders, in which Davros gives them the formula required for their rocket to penetrate the reinforced Kaled dome. The Doctor fails to prevent the rocket from being fired, and the Kaled dome is destroyed, while the scientific corps are safe in their underground bunker. The Thals begin to celebrate, but then Davros orders the Daleks to move in and exterminate them.
The story then involves the Doctor, his companions and a few surviving Kaled and Thal allies, attempting to destroy Davros's Dalek incubator rooms, while avoiding active Dalek patrols.The Doctor and his companions are captured at one point, and Davros forces the Doctor to provide him with details of all the Daleks future defeats. During this interrogation, it becomes clear that Davros is quite prepared to wipe out all life in the Universe. An act which he thinks would "set him above the gods". And he believes that with the Daleks, he will have that power.
The Doctor and his companions, however, escape, and the Doctor sets explosives in the incubator rooms. He has the chance to detroy the Daleks forever, but hesitates due to his ruvulsion at commiting genocide, even againtst the Daleks. He finally decides against it when a member of the scientific corps tell him that they will force Davros to end his experiments.
At a meeting with Davros, they put forward their ultimatum. Meanwhile the Doctor retrieves the time ring and the tape with details of the Dalek defeats (which he destroys with a Dalek gun). Davros summons a Dalek patrol who exterminate everybody at the meeting except Davros and Nyder.
The Doctor sees this on a monitor, and hurries to complete his destruction of the incubators. A patroling Dalek, however, traps the Doctor, but in doing so glides over the detonation wires, and the incubators are destroyed. Meanwhile back in the meeeting room, Davros realises that the Dalek production lines have been started, and asks who gave the order. he believes that only he has the authority to give such an order. The daleks, however, see him as just another inferior being, and exterminate both Davros and Nyder (although Davros survives due to his life support chair keeping him in suspended animation)
In the penultimate scene, a Dalek makes a chilling speech, saying that the will rebuild and consolidate, and when they are ready they will leave their bunker to become the supreme beings of the Universe.
The Doctor, Sarah Jane and Harry grasp the time ring, which transports them through time and space - back to Nerva and the tardis, while the Doctor explains that by destroying the incubator rooms, he has only set the Daleks back by around a thousand years. So the mission is only partially successful.