Reply-Code Omega is a signal that Algalon the Observer could send to the titans, signaling planetary re-origination. According to the Archivum Console of Ulduar, Reply-Code Omega is one of two possible reply signals following by planetary diagnostics after the arrival of Algalon.
"Planetary re-origination" would result in the destruction of modern Azeroth and its reconstruction from the raw materials, recreating Azeroth from the original Titan blueprint. The re-origination device itself, the Forge of Origination, is located in the Uldum desert. Given the death of Prime Designate Loken, the corruption of the Titanic watchers, the destruction of the Well of Eternity, the corruption of one Dragon aspect and the death of another, and the release of the Old God Yogg-Saron, the chance of Algalon sending such a signal is estimated around "99.99%, repeating of course".
Algalon has stated that he has signaled for planetary re-origination at least several times in the past, resulting in the destruction of entire planetary systems (i.e. an entire world), and over time, the combined deaths of a "million-million lives".
In reality, once Algalon has been summoned to a world, he does not actually have to send Reply-Code Omega: if there is no reply code from him within a certain amount of time, planetary re-origination will proceed regardless from Uldum. This is why, having rearranged the reply code from Omega to Alpha after his defeat, he urges haste in sending Reply-Code Alpha in his stead. This "automatic re-origination", as it were, is likely a fail-safe in itself should Algalon be incapacitated (likely by the very problem that caused him to be summoned in the first place) while performing his planetary diagnostic.