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The Fifth Doctor visited Gallifrey to tell the Time Lords that Morbius was launching a plan of galactic conquest — a visit complicated slightly in that he was visiting the Gallifrey of his personal past at a time when he was still on the run. He proposed that Morbius be defeated by a military campaign as the best means of undermining Morbius' authority without more desperate measures such as killing Morbius in the past. The Doctor was selected as the only viable candidate with the tactical and species experience capable of bringing together the many military species who could oppose Morbius's army.
Using his experience of other races — and with the Time Lords funding his army — the Doctor recruited the Sontarans and the Draconians to his army. This first recruitment was aided by staged attacks on Sontaran and Draconian forces by the Time Lords that gave the impression that Morbius was already attacking these races.
Subsequently, the Doctor mounted a counter-attack against Morbius. He lacked the numbers to attack Morbius directly or stage diversionary attacks to keep him distracted. He proposed that they re-trace Morbius' path of conquest, re-taking planets he had conquered. They would add those planets' strength to their own while weakening Morbius' position.
While campaigning against Morbius, the Alliance was joined by Ice Warriors, Cybermen and a squad of Ogrons. The Doctor appointed the Ogrons his personal bodyguards to avoid the jealousy that might have arisen had he selected bodyguards from the other races in the Alliance. The Ogrons called him "Supremo" as they couldn't pronounce his full title of Supreme Co-ordinator.
This plan continued until the Doctor's forces retook the planet Sylvana. There he found his companion Peri Brown. She had been separated from him before Morbius launched his campaign of conquest. This last defeat prompted Morbius to halt his expansion and entrench his position on Karn for the final battle so he could claim the Elixir of the Sisters of the Flame.
The mixed nature of the Alliance forces against Morbius' purely humanoid army gave them a significant psychological advantage. Morbius tried to defeat the Alliance by recalling his still-dispersed forces to Karn for a final assault. The Doctor summoned back-up from some of the planets he'd saved. The resulting battle ended in the destruction of Morbius' army and his own capture.
Some Time Lords suggested the Doctor use the Alliance to establish his own power over Gallifrey. The wounds of his men had been treated and the funeral of Battle-Major Streg took place. This was a unique break from traditional Sontaran custom at the request of the Supremo in acknowledgement of Streg's sacrifice during the battle to save his life. The Alliance disbanded after the Doctor's departure. Each species returned to their own empires. (PROSE: Warmonger)