Unlike the other incarnations of the item, the Scepter is not said to be related with Simultaneous, Renet, or any other associated characters. Instead, it is bought by April as a gift to Splinter. In feudal Japan, Kenshin also holds the scepter, causing him to switch places with April, landing him in the present, while she travels to Japan. The scepter later briefly appears in the memorial closet of Master Splinter during the closing scenes of the 2007 animated movie.
The Time Scepter first appeared in the third season episode Time Travails. In the 2003 Series the Time Scepter is described as "Having a mind of it's own" as Lord Simultaneous explained to the Turtles. An example of this is in the episode The Real World, Part 2 Where the Time scepter, Combined with the Ultimate Daimyo's War Staff brought the Turtles together and the helped destroy Ultimate Drako.
In the Return of Savanti, Part 1 it also became clear that the Time Scepter can "overheat" probably due to over use or being so sencitive to a sudden and dramatic change in the timeline and in  it is also unbelevably durable!
The Time Scepter makes a re-appearance in the packed-in comic book for Teenage Mutant Ninja Turtles Smash-Up, where Donatello uses it in an attempt to instantaneously transport the Turtles, Splinter, April, and Casey to The Shredder's Japanese headquarters. The Scepter malfunctions, and the group ends up hopping to an Amazon rainforest and feudal Japan before finally arriving at their destination.