The story started with Darkseid playing with minifigures of various DC Comic heroes. Jason witnessed Duela Dent being killed by a rogue Monitor, named Solomon, who want to kill people in the "wrong" reality. Bob, another Monitor, went to the Source Wall, which tells him that a "Great Disaster" is coming and Ray Palmer (the former Atom) is needed to stop it. Jason and Donna Troy (former Wonder Girl) talked and Forerunner (an agent of the Monitors) tried (and fails) to kill them. Bob, Jason, Donna and the current Atom (who is leaves and is replaced by Kyle Rayner) looked for Ray Palmer, who in another reality. They hopped to reality to reality but basically get Ray Palmer is another reality. The Jokester, an good guy version of the Joker, joined, but died soon after. Solomon tried to kill them, but Monarch, who hates the Monitors, is gathering troops to fight the Monitors. Jason seemly shot Donna and turned evil. Mary Marvel was now powerless. Madame Xanadu tells her not to go to Gotham. Mary does so anyway and meets up with Black Adam, who gives her powers, which makes her evil. Mary meets a poop-eating demon (I'm not making this up) and defeats it. Mary meet various mystics to try to understand her powers. Eclipso was making Mary do random evil things. Trickster and Pied Piper tried to go undercover in the Rogues (enemies of the Flash) to take them down, but accidentally killed Bart Allen. The duo got tied together by high tech handcuffs and tried to avoid the capture by Suicide Squad. PP turned out to homosexual and the Trickester was homophobic. Jimmy, while investigating Dent's death, discovered he's gaining knowledge for no reason and the ability to gain super powers when in danger. Jimmy got sidetracked so he can investigate the death of the New Gods. Jimmy tried (and failed) to find out why he has his powers only to be kidnapped by Forager, a New God supporting character, so they can work together. Holly Robinson is invited to a woman shelter by Anthea (Granny Goodness in disguise) on the former Paradise Island. GG wants to make Earth women to Darkseid's army. Holly meets Harley Quinn. Karate Kid does random things in the present (he's from the future). He turns out to be infected by an unknown illness and cannot go back to the future. Triplicate Girl tries to aid him to find a cure for KK's illness. They meet Buddy Blank (the former OMAC), because he has a super computer called Brother Eye. They (including Blank and his son) end up in Bludhaven. Injected randomly in narrative are scenes with the Monitors debating if they should do something. This first half of the series was noted for major plot points happening outside of the comic like the death of the New Gods.
The second part is often seen as the better half of the series. This is mainly due to dropping the tie-ins and focused on the actual story. However, this part of the series was still critically panned. The Monitors (all 70 of them despite there suppose to be only 52 of them, including Bob) debated if they should do something. Karate Kid and his team meet Firestorm and they discovered there something under Bludhaven. Jimmy and Forager went to Apokolips (a planet ruled by Darkseid). Bob teleported his group away including Jason (who seemed to change sides). The Monitors decided to do something. Bob's group were teleported to wasteland. It turned out that Jason's killing Donna was fake out to distract the enemy long enough for them to flee. In a previous, "happy" reality, this reality's Lex Luthor and various other people were killed by adult, time and space-punching Superboy Prime (now called Superman Prime). He DESTROYS THE ENTIRE REALITY. He tortured Mr. Mxyzptlk (ignoring the latter's god-like reality warping). Bob's group went into the Batman Beyond universe and finally found Ray Palmer on Earth 51 (a paradise Earth). It turned out this universe's Ray Palmer was killed and the our reality's Ray Palmer replaced him. It turns out that Bob wanted (completely out of the nowhere) to KILL Ray Palmer. It turned out Solomon and Bob were working together and Bob was going to lead Solomon to Ray Palmer, who was the "key" to having the Monitors merge together (this creates a plethora of plot holes). It turned out killing Duela was just to start this plan. Monarch and his army came to Earth 51 and killed the passive heroes of this Earth and the reality itself. Ray Palmer revealed that it was the dead Ray Palmer who was suppose to stop the Great Disaster. This world's Batman made Jason into Red Robin (a reference to the much better than this Kingdom Come series). Superman Prime arrived on the Monitor's base and demanded to be taken to the "perfect" Earth. Its revealed that the Earth 51 Ray Palmer was immune all illness. This Earth's Justice League discovered a living germ called Morticoccus. This Ray Palmer, fearing there could be other Morticoccus(es), went to work in attempt to give every reality at least one person with his immunity. Superman Prime discovered the "perfect" Earth is the one being destroyed and flew off to it. When confronting Monarch, Superman Prime gave the most infamous line of this entire series: "I'll kill you! I'll kill you to DEATH!!!". Monarch and Superman Prime duked it out. The rest of Bob's group got a message to go "to Apokolips". A nameless Monitor took them there. Superman Prime accidentally broke open Monarch's armor unleashing energy destroying all of Earth 51, but Superman Prime survived. Karate Kid's health started to decline, but claimed he knew their was a bunker under Bludhaven. In said bunker, Professor Stein, a supporting character of Firestorm, was being tortured by Desaad. Desaad took over Firestorm's powers, but Karate Kid's gang managed to free his powers. Desaad fled to Apokolips. The gang accidentally activated Brother Eye (I have no idea how), which merged with Desaad's left over tech and send itself and our gang to Apokolips. Trickster and Pied Piper were stilled in the same situation as we last saw them. Trickster got shot and died. This causes the cuffs to active a 24 hour to exploding countdown. Piper used his flute to slow down the countdown. Piper (still cuffed to Trickster's dead body) went into the desert and hallucinated that the body was talking to him (complete with offensive gay jokes). Pied decided to cut off the arm of the Trickster so he wouldn't have to drag the body. Piper was teleported Apokolips (noticing a theme?). On Apokolips, Jimmy was still a slave. Eclipso handed Mary off to Darkseid, only for her to rebel and leave. Eclipso convinced her to give Darkseid's job a chance. But, the next issue had them fighting and Mary rejecting her offer. Jimmy used his powers to free Forger and himself. Forager's first reaction was to kill Jimmy for hitting on her, but she calmed down before she could so. Jimmy used his powers to escape (with Forager) to Earth, where they made out. Mary gave up her powers in regret for her misdeeds. Mary (who was in midair) fell into a sea outside where "Athena" is training the women. Holly and Harley discovered Hippolyta, former Queen of the Amazons. She teams up with the duo so they can defeat the false Athena. Forager revealed she think the soul of the New Gods are in Jimmy's body (hence his powers). Hippolyta's group gain Mary as a member. Jimmy discovered Forager left and left a message to go "to Apokolips". Its revealed Solomon and Darkseid manipulated the whole thing as part of a bet with the power of the "power of Multiverse" being the prize. Hippolyta exposed Athena as Granny Goodness. After GG used her powers to create a portal to Apokolips, Holly, Harley and Mary gave chase. Desaad revealed that Piper's mind-controlling music is actually a musical version of the Anti-Life Equation. Our female heroes freed the Greek gods, who Goodness imprisoned. The gods gave them powers and restored Mary's powers. Brother Eye started to merge with Apokolips. Morticoccus turned out to be Karate Kid's illness. Pied Piper somehow used his music to blow up Apokolips. While Darkseid and Solomon were gloating, Atom overheard their plot to unleash the Morticoccus virus so they can recreate the universe. The heroes had a debate over if they should kill Karate Kid. Solomon revealed Darkseid put the souls of the New Gods into Jimmy so he could have them for himself. Solomon accidentally teleported the heroes to the wrong reality when he got annoyed by their yelling. Despite the heroes' best effort, Morticoccus had mutated due being in Karate Kid's body thus making it impossible to cure. It started to spread and caused humans to become animal-like and vice versa; and caused full scale nuclear wall. This reality's Green Lantern accidentally spread the disease into space. So, the Great Disaster happened... and DC didn't have it guts to have it happen in the MAIN reality that the readers actually care about. This is basically an excuse for Planet of the Ape-style Kamandi, the Last Boy on Earth to not be in continuity. Buddy hid his son in the bunker as Triplicate Girl was killed by rats. The remaining heroes returned to their home world... and this is NOT the end. The heroes spilt up to prevent their world from being effected by the Great Disaster and to get on with their life. Darkseid corrupts Mary with "evil" power of Black Adam. Mary kidnapped Jimmy. Donna and Kyle tried to explain what is going on to the Justice League. Superman (not Superman Prime) arrived to save Jimmy. Ray Palmer shrank into Jimmy's body and altered it to allow him access to all the powers. Jimmy use this to turn into a giant, turtle boy. Orion, Darkseid's son, comes out of nowhere and gets killed, but kills Darkseid with him. In the epilogue (the last issue), Pied Piper somehow is alive; Donna, Kyle and Forager decided to "monitor the Monitors"; and Holly and Harley look at an oversized moon.
My sources was the Atop The Fourth Wall Episodes "Countdown Prologue", "Countdown Part 1" and "Countdown Part 2"; and Wikipedia "Countdown to Final Crisis".