Second Omega Crisis

The Second Omega Crisis was the incident in which Omega returned to threaten Gallifrey for the second time, (TV: Arc of Infinity; PROSE: A Brief History of Time Lords) following the First Omega Crisis. (TV: The Three Doctors)

The Crisis
Though he was once more thought destroyed, Hedin of the High Council contacted Omega to help him. Omega had gained control of the dimensional gateway known as the Arc of Infinity. Through the Arc, he had a gateway between his own universe and the universe of matter, though he still had no physical form. Omega also had a TARDIS and a servant he had created, the Ergon. Omega needed to bond with another Time Lord using his biodata extract. (TV: Arc of Infinity)

On Earth at the time, Omega sent the Ergon to survey the planet, and it ended up in Perivale, where it met Dorothy McShane working in a fast food restaurant. She didn't realise it was an alien, and gave it some fries, which it took back to Omega. Omega didn't like them, claiming they didn't have any salt on them. (PROSE: Anti-Matter with Fries)

Hedin transmitted to Omega the biodata extract for the Doctor, by this time in his fifth incarnation. Omega established a base in the Earth city of Amsterdam, navigated the Doctor's TARDIS into the Arc and began to link the Doctor's biodata with his own. The Doctor faced execution on Gallifrey to stop Omega's return. This was part of Omega and Hedin's plan: they rigged the execution to hide the Doctor and Omega in the Matrix, safe from Time Lord detection.

Omega shifted the Arc to Gallifrey in order to gain control of the Matrix and used its power to create a physical body for himself. The Doctor tracked him down and sabotaged his equipment in Amsterdam, forcing Omega to step into the physical universe before the transfer was made stable. His new body, a replica of the Doctor's, began to decay and revert to anti-matter. Thwarted and maddened by defeat, Omega willed the acceleration of his conversion to anti-matter to destroy the Earth rather than return to the universe of anti-matter but was destroyed by the Doctor using the Ergon's matter converter. (TV: Arc of Infinity)

Other information
A Clara Oswald splinter witnessed the Doctor's confrontation with Omega in the Matrix. (TV: The Name of the Doctor)