Infiltration protocol
Siege Mode is a military configuration used by the Decepticons in the latter stages of a planetary conquest. And if you're a native -- or an Autobot -- it's bad news.
IDW Comics continuity
The Decepticons, under Megatron's command, follow a carefully staged process of infiltrating and conquering inhabited planets. The staged conquest is highly secretive, with soldiers under strict orders not to break cover till late in process.
The protocol has six phases, though few have been described in the fiction thus far.
Phase One presumably comprises the initial infiltration of a planet's society and gathering of intelligence. The Transformers have been on Earth for three years by the time Ratchet meets up with Verity, Hunter and Jimmy; Phase Two appear to be in its early stages by that point.
Phase Two involves the aggitation of pre-existing conflicts and igniting "international hotspots". Frequently this is accomplished with facsimile avatars -- artificial duplicates of key members of the planet's native population, equipped to duplicate the original's actions, memories and personalities, but programmed to serve the Decepticons' interests. The goal is to get the natives to obliterate themselves, without the Decepticons' direct involvement.
Phase Three and Four have not yet been described.
Phase Five is when Siege Mode is typically initiated. Secrecy is no longer paramount, as evidenced by the enormous and highly visible cliff-side command bunker that Starscream's crew erected in Oregon, as well as Runabout and Runamuck's flagrant and unconcealed attacks on Ratchet. Outright military protection of assets appears to be the goal of Siege Mode. Ratchet states that he has only seen this phase once before, though whether this is due to his normal role as a non-frontline combatant or because of other circumstances is not clear.
When Starscream's unit on Earth broke protocol by engaging Siege Mode too early in the infiltraion, Megatron himself arrived on-world to investigate and apply some Decepticon-style dicipline. Having put Starscream out of commission, he promptly downgraded the operation back to Phase Two.
As for Phase Six, well... Ratchet claims you don't want to know if there's a Phase Six.