Tomorrow Dies Today begins just after the return of Steve Rogers. Rogers is back from the dead and has handed over the shield to Bucky Barnes. Wolverine took Rogers' death, (his second death), extremely hard and is still having a hard time with his emotional state now that Rogers is back. Wolverine insists on Rogers coming with him on a world-wide pub crawl and they head out in the Blackbird with Nightcrawler helping out as "designated driver".
As the two friends make their way across the globe Deathlok shows up and is on a mission; seeking out various mutants for execution. Once the pub-crawl is over, Wolverine is approached by a young woman named Miranda Bayer claiming to know the future and who then warns him that there's not one, but many Deathloks out killing people with super powers.
At this point it is revealed that the story is really taking place 20-25 years in the future with present day being in the past. Wolverine is one of the last surviving mutants in the world and has joined up with an underground military group that is attempting to fight the cyborgs. Miranda Bayer is the squad leader and they have discovered that the cyborgs are being sent back in time, by a company called Roxxon, in order to execute all the super-heroes they can. This company has come to not only rule Earth, but much of the known universe as well, by exterminating every threat to their power. The group Wolverine has joined is headed by an unknown person called "the General" and they gear up for a mission to finally destroy the machine being used for time travel by Roxxon.
The future timeline reveals that Roxxon based their work on that of Dr. David Heimerdinger, (former H.A.M.M.E.R. scientist who created cybernetic, zombies for Osborne during the Dark Reign) and have been creating the cyborgs using the bodies of psychopathic murderers. As more cyborgs are sent into the past, present day heroes begin assembling to battle the growing threat with Captain America, Wolverine, Spider-man, Thing, Spider-woman and others teaming up.
One cyborg in particular is shown to still be conscious behind the AI that is controlling his modified body. The back story of how he was a convicted murderer, his rebirth as a cyborg and his ongoing murderous rage plays out in conversations with his AI controller. While the AI strives to understand human emotion and wants to expand what makes it unique, the mind of its host body is proud of the nearly 350 kills he has so far. He is the main cyborg that is fighting in the past as his blood lust helps him excel in his task. The present day Miranda Bayer is not telepathic but has instead been fed memories by her future self using the same time-displacement technology that Roxxon has been using. Once "the General" discovers the previous identities of the cyborgs his people are facing, he uses that technology to inform the younger Miranda. She seeks out the child that will become the cyborg leader and decides it would be better to murder the child than let that happen.
As she holds the child at knife point, in front of the monster he will eventually become, she realizes that no matter what, she is not a monster and instead of killing the child, decides to right the wrongs that have lead to this child becoming that monster. The future Miranda is shown fighting her way to the time machine when she realizes that the cyborg she is fighting is the same one she once showed compassion to. She allows herself to be killed in order to show this AI what sacrifice truly means. She gives up her fight to this cyborg knowing very soon it will witness her doing the opposite to the child she once held hostage. As she dies she demands that the cyborg finally seek out the answers to the questions it has always had regarding human emotion and what it means to not only care, but to finally ask 'Why?'. Miranda believes that doing this is the only way to ensure, that in the past, this cyborg finally makes the right decision. Once the AI has this awakening of the mind it takes control of the host body and helps the heroes defeat all of the other cyborg assassins before going his own way. The AI claims, as he walks away, "for the first time in my existence I am excited at the thought of tomorrow".
After the battle has been won, the heroes wonder if they did indeed change the future. This question is answered as the secret identity of "the General" is revealed. After showing his face he begins to take in all of the sacrifices his people have made and realizes that he himself must make one final sacrifice in order to ensure that the actions of those he cared about, that were made for a better future, were not made in vain.