Rutan-Sontaran War

The Rutan-Sontaran War was fought between the Rutan Host and the Sontarans. It lasted for thousands, perhaps millions, of years, and was waged across the Universe.

Origins of the War
The Sontarans, not yet a species of clones, were already, in the Seventh Doctor's words, a "fierce, martial race". They began to sweep over Mutter's Spiral. Only the Rutans opposed them. Reacting to this, the Sontarans stopped reproducing naturally and turned themselves into a clone species. (COMIC: Pureblood)

A definitive date of the start of the war remains unknown. The Tenth Doctor described it having begun fifty thousand years before 2009 AD, clearly a rough estimate. (TV: The Poison Sky) Field Major Kaarsh gave the same figure in 1605. However, the Rutan known as Lady Winters gave the contradictory figure of ten thousand years, which would mean that the war would have begun circa 8395 BC. (GAME: The Gunpowder Plot)

The Seventh Doctor described this event as "ten centuries" before the 25th or 26th century, meaning that the conflict would have begun in the 15th or 16th centuries. (COMIC: Pureblood) This contradicts evidence given elsewhere, such as a Sontaran speaking of war with the Rutans in the 12th century (TV: The Time Warrior) and the Rutan plan to destroy the Sontarans in the 13th century. (GAME: The Gunpowder Plot)

The Rutans and Sontarans both involved themselves in the Millennium War of 150 million years BC. (PROSE: The Quantum Archangel)

Events of the War
During the 13th century, the Sontaran Linx claimed Earth for the Sontaran Empire. He was unable to hold the planet, and was killed after being stopped by the Third Doctor. (TV: The Time Warrior)

Around the same time, a Rutan ship containing two doomsday weapons collided with the Doctor's TARDIS, causing it to crash-land on Earth. The Rutans on board were placed in suspended animation for four hundred years and lost one of the weapons. When they awoke in 1605, they sent out a distress beacon, which both the Sontaran Empire and the Rutan Host discovered. Sontarans and the Rutans raced to retrieve the weapon and use it on the other species. The Eleventh Doctor modified the weapon, as well as a second weapon Charlie stole. He gave one to each race, telling both that if one attempted to use it, they faced a possibility of killing their own species instead of the enemy. (GAME: The Gunpowder Plot)

By the early 20th century, the Sontarans were winning the war. The Rutans, who had once controlled all of Mutter's Spiral, had been driven to the far fringes of the galaxy. In the 1900s, a Rutan scout attempted to establish a beachhead for a Rutan invasion of Earth. The Fourth Doctor prevented it from doing so, also ending the Rutan plans to use Earth as a launching point for their "final assault" against the Sontarans. (TV: Horror of Fang Rock)

In the 1980s, the Sontarans investigated the possibility of using time ships to win the war. They attempted to gain the secrets of TARDISes from the Second Doctor, but were betrayed by Chessene of the Franzine Grig. At the same time, the Sontarans were involved in a battle with the Rutans in the Madillon Cluster, with the Rutans winning this conflict. (TV: The Two Doctors)

In the early 21st century, the Sontarans were apparently losing the war (based on speculation by the Tenth Doctor) and so set about invading Earth turning it into a cloning world. The Doctor stopped their plan, and the Sontaran fleet was destroyed by Luke Rattigan, with Kaagh as the only known survivor. (TV: The Sontaran Stratagem/The Poison Sky)

Circa the late 21st century, the war saw conflict near the Sol system again, leading to the Rutans attempting to capture planet Earth. (PROSE: The Sontaran Games)

During either the 25th or 26th century, the Rutans destroyed the Sontaran homeworld, Sontar, with photonic bombs, though some escaped with the Sontaran racepool. (COMIC: Pureblood)

In the 26th century the Rutans took over the colony of Chelsea 426 above Saturn by using spores from flowers to take over the people. However the Fourth Sontaran Intelligence Division opposed the Rutans and attacked the colony. Due to the Tenth Doctor's intervention, the Sontarans were victorious, although later there was evidence that one Sontaran had been taken over by the Rutans. (PROSE: The Taking of Chelsea 426)

It's unknown if this took before or after the destruction of Sontar.

Involvement of Gallifrey
Gallifrey was involved with the war several times. During the Dark Times, the Gallifreyan hero Prydonius was sent to act as an observer in the war. (PROSE: Cat's Cradle: Time's Crucible)

As early as the Earth's 13th century, the Sontarans had theorised the possible invasion of Gallifrey. (TV: The Time Warrior) They would later turn this into reality with the help of a race called the Vardans and (seemingly) the Fourth Doctor. Although the invasion was temporarily successful, they were ultimately repelled by the Doctor and the other Time Lords. (TV: The Invasion of Time)

Other universes
In an alternate universe, the Warburg, led by General Sontar, the Warburg's supreme commander, and the Rutan Host convened on Gallifrey to meet face to face without violence. (PROSE: The Infinity Doctors)