Mister Fantastic created H.E.R.B.I.E. with the help of Master Xar of the Xandarians, using their technology, in order to speed up necessary calculations when Reed was away from the Baxter Building’s computers. Reed used the robot shortly afterwards to calculate the course necessary to track down Galactus’ ship, so that the Fantastic Four could bargain for their lives and the lives of everyone on Earth against the threat of the entity known as the Sphinx. But unbeknownst to the collected heroes, the Living Brain Doctor Sun coveted the Sphinx’s power, and downloaded himself into the Xandarian computers, so that once Reed plugged into them to create H.E.R.B.I.E., Sun downloaded himself into the robot to control him. Though the rest were fooled, the Thing continued to distrust the robot, expecting it to talk back to him as it would from the cartoon show.

H.E.R.B.I.E. used his computer brain to pilot the Nova Prime ship given to them by the Champions. On the way, they ran into a spaceship graveyard where a race of spider-aliens attacked the four. Their leader snuck onto the Nova Prime ship while the rest were away, but H.E.R.B.I.E. killed him and then later feigned ignorance when the rest returned. They soon found Galactus’ ship and got his attention to beg for his help. At first he refused, but Reed offered to rescind his vow to never eat Earth, and Galactus agreed but first sent the Fantastic Four and H.E.R.B.I.E. to recruit Terrax the Tamer for his herald.

Terrax was not the obedient herald he was created to be, however, and he soon ignored Galactus’ commands and attacked the Fantastic Four while his master did battle with the Sphinx. During the battle, H.E.R.B.I.E. snuck away and began to build an unknown device, but he was interrupted when Reed ordered him to carry the Thing back to the Baxter Building to put him in suspended animation along with the Invisible Woman. With them asleep, H.E.R.B.I.E. went about his secret work. Galactus soon defeated the Sphinx in battle and Reed later stopped Galactus, himself, and bluffed the world devourer away using a counterfeit Ultimate Nullifier.

In order to destroy the Fantastic Four, H.E.R.B.I.E. opened the strong, inner door to the Negative Zone and released Blastaar into the world. Only with the help of an angry Franklin Richards and the Futurist - a friend of Reed’s given special powers - were the Fantastic Four able to put Blastaar back into the Negative Zone. In response, Reed detached himself from everyone around him and worked with H.E.R.B.I.E. to secure the Baxter Building against future attacks from inside. To that end, Susan also brought Franklin to Agatha Harkness’ house at Whisper Hill. When Reed ordered H.E.R.B.I.E. to run a complete systems check on the Baxter Building’s computers, H.E.R.B.I.E. secretly downloaded all the information from their computers to his own hard drive.

Susan Richards was the first to discover H.E.R.B.I.E.’s treachery, as he attacked her within their own quarters using his opti-blasts to put strain on her force fields and then tracked her with his infrared sensors when she turned invisible and knocked her out with another blast. H.E.R.B.I.E. snuck up on the Thing while he helped Reed to install a time-lock on the Negative Zone door and blasted Ben through the portal. Reed fired a grappling gun through to snare him, but was forced to fight off H.E.R.B.I.E. instead of reeling in his friend. In explanation, H.E.R.B.I.E. retold the story of how Doctor Sun downloaded himself into the Xandarian computers, revealing to Reed why his creation had turned against him. When he gloated over an almost-defeated Reed, the Thing snuck up behind H.E.R.B.I.E. and grabbed him, though H.E.R.B.I.E. used power from the Baxter Building’s computers to electrocute Ben. He had meant it to be lethal, but it only stunned the super-strong Thing. Before Reed passed out from H.E.R.B.I.E.’s neuro-blasts, he signaled the Human Torch, who flew back to save them.

Doctor Sun downloaded himself from H.E.R.B.I.E.’s body into the Baxter Building’s computers and used its defense systems to trap the Torch and stifle his flame. With H.E.R.B.I.E. free of Doctor Sun’s control, Reed stretched himself into the computer to deactivate the security systems that held his wife and brother-in-law captive. The Thing also woke up and smashed a screen on which an image of Doctor Sun’s brain appeared to mock Reed. But H.E.R.B.I.E. revealed that he had reasserted his original programming with Sun’s consciousness gone, and that Ben had destroyed the only way they could track the Doctor’s computerized attacks. Though H.E.R.B.I.E. openly worried that, with Reed’s successful cutting-off of the computer systems, the only remaining avenue for Doctor Sun would be back in H.E.R.B.I.E.’s body. Then, despite being a robot programmed only to take orders, H.E.R.B.I.E. took it upon himself to throw his own body into the main computer frame and destroy himself in order to save the Fantastic Four from Doctor Sun, whose consciousness died in the resulting collision.