In the wake of the Onslaught crossover, the Avengers, Hulk, and Fantastic Four were seemingly destroyed saving the world. In actuality they were transported to an alternate dimension by Franklin Richards, son of Reed and Sue Richards. For the last year, they have lived a life similar to their previous one with minor alterations. The time has come to bring the heroes back to the Marvel 616 universe.
Ashema of the Celestials has arrived on Earth and explained to Franklin that her race is aware of the alternate world he created to save his parents and their friends. Impressed as they are, they have decreed that only one world may survive - and he must choose which one.
Dr. Strange has retrieved Franklin's blue ball which contains the Heroes Reborn universe from the Florida swamp. When he brings it back to New York, it makes its way toward the Hulk and pulls the Hulk as well as the unsuspecting Spider-Man into the Heroes Reborn world.
Prompted by the appearance of Franklin, Reed Richards and Iron Man have conclusively proven that the world they live on is less than a year old. Calling in the other members of their college think-tank (including Doom, Banner, and Pym), they come to the sad conclusion that have little choice but to abandon this world and return to their home dimension in Doom's space ship.
Franklin makes the difficult decision that the Heroes Reborn world will be sacrificed to ensure that their original world is safe.
The "original" heroes from the other world are quickly identified and brought to the Baxter Building. Cap and Falcon must explain to Rikki Barnes aka Bucky that they have to leave and she must remain behind. Iron Man makes a special trip to say a "special" goodbye to Pepper Potts.
While making preparations, Richards confront Ashema and tells him that their son will remain with them once this voyage is complete. He is backed by Thor and many of the other heroes. Initially Ashema considers destroying them all for their arrogance. Her eyes meet Franklin's and she changes her mind. She agrees that his world will continue to exist. Thor overplays his hand and is temporarily turned into a frog. Ashema explains the new agreement: they must all leave this world or it will be destroyed.
The heroes board Doom's ship which has been fitted with Richards' shrinking technology. Richards explains that the way out is through the Negative Zone. The border of the Zone is the limits of Franklin's imagination; their world lies on the other side. The ship must be shrunk down to fit into the portal inside Richards' lab. As they take off, Doom stares in admiration at the power contained in the child.
Just before they cross back to their reality, Doom betrays the group and kidnaps Franklin and escapes the ship into the Negative Zone. Franklin reminds Doom that Ashema said that they have to leave as a group. Doom insists that with his genius and Franklin's powers, they can handle the Celesitals. Thor attacks Doom separating him from Franklin, allowing Richards to grab his son. To ensure that none of his allies die as a result of Doom's actions, Thor opens a portal into another dimension and drags Doom in with him.
Once Franklin is back inside, the shrinking field goes off-line. The ship is being torn apart by the sudden, uncontrolled growth. As the heroes near their home dimension their memories return to them. Some are content with their lives; others are disappointed with themselves.
As the ship breaks apart they run the very real risk of being trapped in this dimension without the ship to propel them through the border. It is at this point the trans-dimensional energy emanating from the Hulk brings him into proximity to his separated "other" Bruce Banner. The energy merges the two beings back into one. The energy from this fusion tears a hole in the Negative Zone and in the resulting vacuum the heroes are pulled back to their home. They last at various places across the globe due to the imprecise nature of their method of transportation.
Ashema returns to the Celestials with the "results" of their experiment. This has deviated greatly from the expected outcome. Unlike her brethren, she has actually experienced humanity firsthand and has been changed because of it. In order to save the Franklinverse, she has sacrificed her consciousness to ensure its preservation. She remains in a dreaming state while the rest of the Celestial begin to examine the changes brought about by her interaction with humanity.
Through the series, Ashema mentioned that they wanted Franklin to become the newest Celestial. For god-like beings they seem to overlook one important fact: god-like powers does not automatically given someone god-like wisdom. While it would make sense to have powerful individuals train Franklin in the use of his powers, the assumption he was ready proves that even an immortal race doesn't know everything.
2.5 webs. The one question I wanted answered was not answered. 1/2 web off. Unless the purpose was to see how Ashema would handle taking on human traits and then study those changes? Who knows? I am a little annoyed that it was not clearly stated.
Otherwise this was a reasonable conclusion to the series. We know Doom and Thor will return, so there's nothing to do but wait.
At the very least, the Avengers and Fantastic Four have been brought back to the regular Marvel universe.
This is not the first time Thor has been turned into a frog. This occurred during The Mighty Thor (Vol. 1) #364-366
From this point the titles that were part of the Heroes Reborn project were relaunched: