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In Transformers: The Movie (1986), Starscream boldly throws a badly wounded Megatron out of Astrotrain into deep space, and seizes the Decepticon leadership.

Starscream in a crown

Sadly he is murdered at his own coronation by a vengeful Galvatron, but it is still a unique moment in Starscream's character history.

Apart from this one occasion, has Starscream ever, in any continuity, been sole leader of the Decepticons?

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You describe the state of the Deception forces in of most of the first seasons of Transformers: Animated and Transformers: Prime

In Transformers: Animated's three-part pilot "Transform and Roll Out", Megatron is the recipient of Starscream's treachery, and apparently destroyed.

Megatron attacks the Autobot ship and tries to retrieve the Allspark, but when an explosive planted on Megatron by the treacherous Starscream detonates, the ship crashes on Earth. The Autobots go into stasis to survive the crash, while the scattered remains of Megatron are discovered by a human scientist named Isaac Sumdac.

-- Wikipedia, Transformers: Animated.

From the viewpoint of the Decepticon forces on Earth, Starscream is in command from the end of the pilot up until S1E16, Megatron Rising, Part 2.

In Transformers: Prime, Megatron ends the pilot comatose in lunar orbit. Starscream subsequently takes command of the earthly Decepticon forces, which appear to be all that are surviving.

Season One opens with Cliffjumper being murdered by Starscream, who leads the Decepticons during 'Lord' Megatron's absence. Following Megatron's return, he uses Cliffjumper's corpse as a test subject for Dark Energon, which he intends to use to create an undead army from Cybertron’s fallen warriors. The plan fails when the Autobots destroy Megatron’s Space Bridge, leaving him in a comatose state floating through the empty space, and allowing the treacherous Starscream to claim leadership of the Decepticons once more.

--Wikipedia: Transformers Prime

Starscream leads the Decepticons from the end of the pilot, until the end of S1E14, "Out of His Head."

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  • ,+1 Oh wow, "Lord Starscream"? This is what we all wanted! AMAZING! Commented Aug 17, 2022 at 8:46
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    @EleventhDoctor Yeah, these are just the two situations I'm most familiar with. If I'm not mistaken, there's an arc in one of the comic continuities where Starscream becomes the legitimately-selected head of state of Cybertron, but I'm not sufficiently familiar with the comics to give further reference.
    – notovny
    Commented Aug 24, 2022 at 22:25
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In Transport to Oblivion,

Megatron is knocked into the active Space Bridge and is presumed destroyed. Starscream assumes command and orders a retreat.

STARSCREAM: "Megatron is dead! I am your leader now! Follow ME!"

For a short while, though. Megatron emerges apparently unscathed at the Cybertron end of the Space Bridge, and vows vengeance against the Autobots.

youtube

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    +1 Great answer, thank you! I loved the youtube video! Commented Aug 16, 2022 at 9:55

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