What are the best Transformers stories? All from the comics and TV shows. I know majority mentioned the best stories are More Than Meets The Eye, Robots In Disguise, Last Stand Of The Wreckers, The War Within and All Hail Megatron. Also the 1986 Transformers the Movie, "War Dawn" and "The Return Of Optimus Prime" episodes from the G1 tv show. "Code Of Hero" from Beast Wars. And I agree all these were great. To me i'll also add Transformers: Prime was a good show. What else is good story being told from the Transformers comics and episodes from the any of the shows?