The fourth, and final incarnation (until May 26, 2012) of TOM is perhaps the most controversial according to longtime fans of the block. This incarnation has a much smaller body than his predecessor and has a frame with rusted metal and peeling body paint. No longer a visored robot, this is the first and only TOM to have facial features. Creators wanted the new TOM without the helmet, as well as look more organic compared to his past incarnations.

At the start of the tenth year, TOM's hosting responsibilities were scaled back considerably. He was seen only during the opening and continuity promotions, while his new assistants Flash and D direct the broadcast process. In addition, this is the first TOM unit to not have custody of any version of the spaceship Absolution, which had been the base of operations for the block since July 1999.

TOM 4.0 officially ended the Toonami block in September of 2008. D and Flash are seen readying Jungle Base for permanent shutdown, and TOM thanks the viewers, flies away, and says "bang.", a reference to voice actor Steve Blum's previous role as Spike Spiegel from Cowboy Bebop . The speech was as follows:

"Well, this is the end, beautiful friends. After more than eleven years, this is Toonami's final broadcast. It's been a lot of fun. We'd like to thank each and every one of you who made this journey with us. Toonami wouldn't have been anything without you. Hopefully we've left you with some good memories. So, until we meet again, stay gold. Bang."

TOM 4.0 most recently appeared on the revived Toonami block, having a conversation with the current TOM 3.5. Both TOMs stated that they should tell a story someday, about presumably TOM 4.0's origins, and TOM 4.0 stated that running Toonami was all up to TOM 3.5 now. This conversation proved that TOM 3.0 and 4.0 are different individuals and hinted at a possible T.I.E. event in the future.

This incarnation has been criticized very negatively because this TOM doesn't have the same design or a back story like the former incarnations. Also, as of  2012, there hasn't been any online nor on-air explanation about the change in appearance of TOM, though some have made guesses. According to the executives, they didn't have the time to create a TIE when they developed him. Many blame the late night Adult Swim block for Toonami's demise as the block begun airing anime on Saturday nights shortly after Toonami ended, beginning on September 27, 2008. On the same day, Cartoon Network stated that Adult Swim would be its "main source for anime". On December 31, 2012 Creators of Toonami, Jason DeMarco and Gill Austin admitted on the Toonami Tumblr page that they "would definitely want to go back in time and not have a TOM with a face."