The last few epasodes of Armada are GOLD!

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Armada, or Micron Densetsu?

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X Bob, you said the wrong name!!! :P

 

I'll go with More Than Meets the Eye as well.

Ihave a few in mind actually...

 

The Agenda was definitely great, as well as the entire alien storyarc in BW.

 

Also I liked the concept of Megatron's Master Plan. Sure, they episodes were mediocre, but I was always intrigued by the possibility of the Decepticons making an unholy alliance with a human politician.

I'd go for Heavy Metal War. I mean it had everything;

Prime battles Megatron

Megatron cheats(in one of his best plans to date)

Constructicons getting whooped by Dinobots

Devastator battles Dinobots

Holographic illusion of a giant Autobot stunning Devastator

And of coarse one of those "We shall rise again...." endings!!!

Along with "The Agenda" and "Nemesis", I'd go with Dinobot's strained allegiance to the Maximals.  It was one of the high points I watched for the entire series.

 

I agree with XBob as well: the last few eps of Armada were very well-done in my opinion.

The Agenda and Nemesis and More Than Meets the Eye

I dont know about actual story arcs, but I loved the Energon Ep when Megs and Prime had that first energon sword battle, and the GF ep when Megs and Prime fought over the chip square!

MTMTE 1st 3 episodes of course.

Most of BW pretty much pwns this question.  The writing and characters were so far above anything before or after that series.... I wish we could get a Western-culture-produced TF series again.