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- The infiltration protocol is a Decepticon modus operandi in the IDW Publishing portion of the Generation One continuity family.
The Decepticons in the IDW continuity, under Megatron's command, follow a strict infiltration protocol -- a carefully staged process of destabilizing and conquering inhabited planets. The staged conquest is highly secretive, with soldiers under strict orders not to break cover till late in process.
Though brutal in its later phases, this tactic is still constrained by the Code of Interplanetary Conflict.
IDW comics continuity
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The Decepticon infiltration protocol has six phases, though not all have been depicted 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 agitation 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.
On occasion, the Decepticons will encounter unusual resistance, and see fit to use a special protocol known as Mirror response mode, as they did when encountering the Avengers as Phase Two unfolded on Earth. Whether this MO is tied specifically to Phase Two is not known.
Phase Three - Not yet described, though it was mentioned as having been completed at the end of Devastation. Perhaps this is where the Decepticons start having direct involvement.
Phase Four - not yet described.
Phase Five - not yet described. However, according to comments made by Ratchet, it appears that the Decepticon presence is now known at this point, and is usually the earliest that Sixshot will get involved.
A special M.O. known as Siege Mode is typically initiated during Phase Five. Military protection of assets appears to be the goal of Siege Mode, implying that the Autobots and/or the natives are now making efforts to stop the Decepticons through straightforward military force; a massive above-ground fortress (variously known as the siege armature or siege mode armature) is typically installed on the planet and used as a base of operations. Secrecy is no longer a concern, 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. 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.
Breaking protocol is extremely rare, to the point that Ratchet was in a virtual panic when Starscream's unit on Earth engaged Siege Mode too early in the infiltration. Megatron himself soon arrived on-world to investigate and apply some Decepticon-style discipline. Having put Starscream out of commission, he promptly downgraded the operation back to Phase Two.
Phase Six, by all accounts, is pretty much the end of the world. An aside comment by Springer ("I don't care if it's Phase SIXTY!") implies that the Decepticons have achieved Phase Six in the invasion of Varas Centralus: a state of open, all-out war on a devastated planet. Likewise, the flagrantly destructive and powerful Sixshot refers to himself as a "Phase Six kind of 'bot".