When we last saw the time-traveler Bishop, he was lost in the Axis of Time. He's faring no better now, though his journey toward the central control planetoid at the epicenter of the spatial realm is making some progress. Having strolled down the long walkway of light, one among many leading toward the convergence point, a considerable way, but still with far to go, his solitude is instantly cut off by the sound of a familiar, befuddling voice, asking him to guess who. Bishop stops in his tracks, and grabs his head, sighing defeatedly in protest. The gray-skinned, time-displaced wacko who calls himself Bender appears at one side, then another, then crouching below him, and laughing maniacally as he rushes ahead. Bishop gets in the clown's face, telling him he's had a long day, or week, or however long he's been there. As Bender mentions that all walk and no play makes him a dull boy, the walkway of light curls up violently, whipping like a snapped rubber band, sending the two men into the air for a moment, before returning to normal. When Bishop, landing back on the platform safely, asks what's going on, Bender, riding one of the many door-shaped mirrors floating throughout the area, explains in an announcer-like voice that a great being is threatening time itself. The mirror shows a vision of Apocalypse's hands, as he manipulates a long circuitry board, causing pink-electricity to crackle outward. Giving a thumbs up, Bender exclaims with a grin that knowledge is power. An explosive blast of yellow light changes the image on the mirror screen, to that of Cable and Tyler climbing up the side of the cliff, as we saw last episode. Bishop recognizes the mutant from his encounter with him back in season 2, pointing him out, and making Bender ramble off another wild stream-of-consciousness comment.
The scene shifts to that of the mirror's image, where, Cairo, Egypt, 3999 A.D., Cable views the cloaked time machine through computer-scanning binoculars. The defensive dome covering the ship is visible sporadically by a rotating searchlight, just enough for his scanner to properly identify it from afar. To the right of it, amid the desert terrain, a power station is also IDed, the binocular display rapidly zooming inward to inspect the scene closer. Watching this from the top of the cliff, Tyler asks his father if he's ready. Cable lowers the binoculars, and confirms he is, telling the kid to start the ball. Tyler speaks into a walkie-talkie, telling his teammates to give them 30 seconds before losing one power station. He wishes Cable would let him go with him, but his father, putting a hand on the young man's shoulder, mentions that if he doesn't make it, he'll need him to carry on here. Telling Tyler he knows he'll make him proud, Cable leaps off the side of the cliff, and begins to climb down into the valley where the time machine is being kept by the government. Talking into his headset, Tyler reminds his dad that the energy dome will only be down for a minute. At the power station nearby, an explosion bursts out from one of the many structures within the tightly-designed region. Inside the complex, the other three members of Cable's rebel group are behind this attack, blowing up a robotic sentry, before racing down, firing upon another, destroying it, and repeating the process while making their way through the halls. Eventually, they run into a human in a large, yellow, metal exoskeleton, who swipes them aside with his claw-like appendage. Reaching the base of the cliff, Cable notices the dome is still up over the time machine, informing his son of this. Tyler replies that their teammates have run into heavy resistance. Heading toward the dome anyway, Cable stays out of sight, hiding behind well-placed rocks. With two robot sentries patrolling the perimeter, he cocks his laser-rifle, and makes his presence known by firing on one of them. Though he takes the bot down, the second manages to hit him with a stun ray, which cripples Cable with a lingering electric charge over his mostly-cybernetic body. His organic right arm still works, enabling him to touch his communication-link (located in the circle-x symbol on his chest), where he asks his son what's happening. Tyler informs him he's still not getting any word, and while he scans the scene with his father's binoculars, he's distracted by the view, and Cable's stressing of the fact the power station must be destroyed, since it's the only chance they have. This allows a robot sentry to approach him from behind, and by the time he notices him, it begins to fire. Tyler rolls and flips out of the way, pulling out his own lasergun to blast back, blowing the robot into pieces. He thinks himself secure, turning away just as another sentry enters the scene, walking through the smoke of the previous one's destruction.
Below, Cable stares upward at the top of the cliff, seeing the explosions bursting above, as he calls to his son to check on his status. Tyler avoids being struck by the sentry's beams of energy, thanks to some expert maneuvering, but is unable to get a direct hit in return against it. Cable watches closer through his left, bionic-red eye, and witnesses Tyler getting knocked down by a laserbolt. His bodily charge finally ending, Cable climbs back up the cliff in an attempt to rescue his son, until he notices a series of explosions occurring at the power station. Inside it, the metal-armed Kane races down a path, setting bombs along a wall, as a sentry fires down at him from above, until it's caught in one of the explosions. The security dome over the time machine finally falters, dropping the rotating light and stealth shielding to reveal the dome-shaped ship resting in the desert. Tyler's gunfight with the sentry reaches its conclusion, as the robot blasts the ground below him, knocking the teenager off the edge. He falls against another ledge below, not too far above his father, who calls out to him. The sentry begins to fire down at him, and Tyler blasts back, while screaming for his father to get going. Cable vows to come back for his son, and heads back down the hillside, racing across the desert, right for the entrance to the time machine. Once within the entry-corridor, a door ahead slides back, to reveal two more robot sentries waiting for him, firing on sight. Cable leaps off a wall, coming closer to the pair of bots, blowing one up on the way there, and the second with a near-close blank range blast. Once at the control panel near the door, he activates a small keypad on the underside of his left cybernetic arm, causing his hand to gleam with energy. He places his palm over the panel, and the doorway begins to close, just as a trio of sentries charge down the hall. The one in lead ends up with its head and blaster-arm caught in the closing door, allowing it to fire at the intruder randomly. Cable heads to another control panel in the center of the, and pulls the same trick he did on the doorway to it, telling the robot to take his time, since he'll be gone in a minute. The three sentries behind the one caught in the door fire upon their fellow robot until it and the door explode, giving them access to the room at last. Cable, though, has control of the platform, which lowers him down a shaft into the Earth's crust. The sentries fire down at him, but are unable to make contact. The platform locks into a walkway which extends out from the circuitry-riddled hull of the hidden craft. Viewing the time machine fully at last, in all its gigantic, glass-toped dome glory, Cable, calling it "Graymalkin", hopes they kept its battery charged.
Once inside Graymalkin, Cable works the keypad, activating the power, bringing on all the lights. One quick tram-ride, followed by a short elevator trip to a lower level, he reaches the ship's control room. Sitting at the wide computer panel, Cable begins to operate the gearshifts, which cause the massive craft to rise up into the air, before vanishing from the year 3999 in a flash of light! Soaring through the multicolored vortex of the timestream, Graymalkin yaws slowly from its leaning forth position, to slightly back, while lightning-like energy smashes against the glass & green-technology-bottomed ship, which just so happens, with its six claw-like legs, to resemble some sort of futuristic tick. The monitor screen above the control panel counts down the years the craft is passing, until it reaches 2192 A.D. That's when "Guidance Failure" begins to flash, and the color of reality for Cable, who is unaware of what's happening, changes to that of a photo negative. Viewing his plight from a portal-screen in his Axis of Time dungeon, Apocalypse admits that Cable's yearning to destroy his resting place at its inception is a wise stratagem. But adds ominously that first, he has a service to perform. Graymalkin, after passing through the Axis' space, suddenly rematerializes above Xavier's School for the Gifted, the morning following the wedding of Cyclops & Jean Grey. The massive craft's landing on the grounds of the estate causes the entire mansion to shake violently, alerting those within the War Room, Professor Xavier, Wolverine, and Storm, to the arrival of this visitor. By the time they reach the ship, perched on its four pincher-like legs, Cable lowers on a hovering platform from the craft, wondering what he's doing there, which Xavier mentions he was about to ask him as well. Soon, in the War Room, having heard the backstory of recent events offscreen, Cable replies that he doesn't care about missing psychics and "time jolts", since he's only after Apocalypse. The Professor calmly explains that the immortal being was involved with at least one of the kidnappings, meaning their interests coincide. Blithely remarking that they're boring him, Cable tells Xavier that if he wants to help him nail Apocalypse, to get his team together, so they can get started.
Meanwhile, in Beast's lab, he runs a computer simulation, showing a colorless male figure amid a long, featureless tunnel. The mutant scientist explains to Shard, that it's conceivable that a powerful force traveling through time creates a backwash, a kind of wake that disrupts the paths of normal time travelers. She's less than impressed by this, since it's just a theory, and he has no evidence that this happened to her brother. Beast explains that Bishop's disappearance in time fits the computer model perfectly, showing a second male figure on the onscreen simulation, passing the first one, and causing a rippling in the waves around them. He points out the effect of the more powerful time traveler on the first, causing it to change directions. Elsewhere in the mansion, Cyclops and Archangel approach a tightly-sealed holding chamber. Scott places his gloved hand to a panel, and in a registering flash, with an electronic beep, the thick, reinforced door opens, allowing the two mutants to enter the dark cell, where Sabretooth is behind held, bound into a large metal chair, with a steel mask over his mouth. He becomes aware of his visitors, when Cyclops tells him he's too stupid to have planned the scheme on his own, asking who he's working for. Sabretooth, calling him a pretty boy, tells him to suck rocks. Wolverine walks in, telling the team leader that Professor X wants him in the War Room. Figuring he's wasting his time there, Cyclops departs, along with Archangel, leaving Logan alone with his old enemy. Hitting a control button, Wolverine frees Sabretooth from the restraints holding him to the chair, and popping his claws, he suggests he and the "hairball" talk. When Creed lunges at him, snarling, the X-Man hits another control button, sealing the door behind him, leaving the fierce battle between the feral foes to our imagination.
Soon, in the operations center of the X-Mansion, known as the War Room, the ten assembled mutants gather around a red-lined hologram schematic of the pyramid base of Apocalypse. Cable explains that it's called the Lazarus Chamber, and that he discovered it... or rather will discover it, in about 2000 years from the present day, and adds that it's the secret of Apocalypse's longevity, since he goes into hibernation there every hundred years. A flashback shows the immortal mutant, lacking his usual blue costume, instead wearing Egyptian attire, as he enters the pyramid's inner chamber. Upon lying within a tomb at the center of the room, Apocalypse is sealed inside by the ancient, alien technology, with a layer of light guarding the darkened chamber. As the flashback ends, Archangel feels vindicated by this revelation, noting that his own research showed periods of inactivity for Apocalypse, but he could never figure out why, nor where he went. Cable informs the X-Men that he destroyed the chamber in his own time of 3999, but before he did, the endless enemy grabbed his time travel device, and can just return to any time before it was destroyed to rejuvenate. The white-haired, partial-cyborg mutant announces his plans to go back to when the pyramid was first built to get rid of it then, to which Archangel eagerly exclaims his approval. Cyclops brings up Sinister and the missing psychics, and Cable tells him to find someone who cares, since he left his son back in the future so he could get at Apocalypse, and may never see Tyler again. When Scott argues that there's more to this than just him, further confrontation is quelled by Wolverine, who enters the room dragging Sabretooth behind him, and tells him that no, there isn't. He reveals that Sabretooth is working for Apocalypse, and everybody might be. Beast thought that their prisoner refused to talk, and Logan, tossing the unconscious (but groaning weakly) mutant named Creed onto the floor, claims that he changed his mind. Xavier asks what else he said, since the pieces of the puzzle don't fit, wondering why Magneto would be involved with Apocalypse. Wolverine, mentioning that it took an hour just to get that much out of him, suggests that if he wants more, he knows how to get it. Having chosen not to enter the minds of others without their consent, the Professor hesitates. Cable urges him to get the information out of him, since it's important, or else he'll do it himself. Left with no other option, Xavier telepathically enters Sabretooth's mind, seeing images of the Axis of Time, Apocalypse, a giant clock-face, Mr. Sinister, Magneto, and various time portals. Once the brainscan ceases, Professor X realizes that Cable is right, and they must stop him, at all costs. Beast asks his teacher what he saw, and he tells him, adding that Apocalypse is bent on mastering time itself, and has persuaded some of the most powerful mutants on Earth to help him. Cable declares that if they take out his life-support system, then none of this will have ever taken place, with Xavier agrees with. Cyclops orders Rogue and Jubilee to stay behind with Shard, who questions this decision, offendedly asking if they don't think she can handle it. The Professor assures her it isn't that, but if they fail, her time travel ability may be her brother's last hope. Archangel wishes to go, and though Xavier tells him there's no room on this mission for vengeance, Wolverine argues that revenge can help one's focus. The winged mutant claims that such a path is not for him anymore, since he knows just what's at stake.
Momentarily, the X-Men join Cable in Graymalkin's control room. The massive craft lifts into the sky, and once high enough, it reenters the timestream in a blink of light. Viewing this from the Axis of Time, Apocalypse calls those he's spying on "tiny, meddling insects", claiming that they don't realize that he who controls time, controls every eventuality. Mystique approaches, saying that he summoned her. He confirms this is true, and remarks that the endgame has begun. Inside Graymalkin, the endlessly shaking journey through the void of time rattles Wolverine, upsetting his stomach. Elsewhen, in the outer fringes of the Axis of Time, Bishop is quietly walking along the walkway of light, when Graymalkin suddenly zooms directly over his shoulder, knocking him off his feet from the close impact. After the time machine passes into the era it seeks to reach, it appears in Cairo, Egypt, the year 1200 B.C, floating in the blue skies above the sandy desert. Finally landing on a cliff overlooking the Nile Valley, Cable tells his new partners that Apocalypse's pyramid is just over the rise, down-river. The X-Men, and friends, exit Graymalkin, where Professor X tells Storm to take Archangel to scout ahead to see if the pyramid is guarded. The pair of flying mutants do so, taking the high road, while the others take the low road, and as the sun sets on the horizon, the two reach their destination before them. In awe over the sparkling red glow over the Nile River, Storm notes how beautiful it is, mentioning that her parents loved this land, and though her life was hard after they were gone, she loved it, too. Noticing that the pyramid seems to be unguarded, she tells Archangel to bring the others up while she makes sure. After night has fallen on the desert domain, the gang of time-traveling mutants regroups. Beast tells Cable that his timing is perfect, since the stone blocks at the base of the pyramid suggests that construction has recent been completed. Professor Xavier asks for a diversion to cover their approach, and Storm gives it to him, causing the winds to howl and rage, lifting the sands of the terrain into the air, spinning them into a focused whirlwind. As Cable adjusts his laser-rifle, Cyclops tells him how sorry he is about his son, saying he knows what it's like to lose someone you love. The gruff soldier responds only by declaring that he hasn't lost Tyler, yet. Scott asks Xavier if he knows anything more about why Apocalypse is kidnapping psychics, and Cable rises to his feet, asking who cares, since he's pure evil, and that's why he has to go. Beast comments that if Apocalypse is indeed the personification of evil, it may be impossible to destroy him, since the conflict between good and evil is part of the fabric of existence. Suggesting that the world might not be able to exist without evil, and if Apocalypse is destroyed, evil may only take another form. Replying that he'll worry about that later, Cable is first to set off into the unnatural sandstorm.
Upon reaching the base of the Apocalypse-faced pyramid, Cable points out the entrance is behind one of the stones. Utilizing his incredible strength, Beast pulls back the large brick, unveiling the hidden passageway. Once he suggests they see who is at home, he's struck in the back by a laserbolt! Racing through the air on metal, hovering horses, the Four Horsemen of Apocalypse greet the visitors from the future with their advanced weapons drawn. Archangel points out that Cable was right, that the immortal protected himself. The X-Men dodge searing laser bolts from the Horsemen, who, as evident by their Egyptian style attire, are an incarnation of the foursome never witnessed by these mutants prior. Recovering quickly, Beast leaps out of the way of Pestilence's rain of charges, picking up a stone brick and hurling it at her as she flies on her horse, deflecting her direction away from him. War flanks between Cyclops & Cable, soaring down at the pair, avoiding their blasts, until Scott makes contact, knocking the being off its flying horse. On metal wings (thus needing no horse), the Horseman called Death swoops toward Storm, hitting her in the back with a bolt from his laser-scythe. When he returns to finish her off, Archangel, who was Death himself once (or will be one day to this ancient incarnation), distracts the creature from his target. They face off in the skies, where the blueskinned mutant tells the silent, skull-faced being that there's no use fighting, since he had his job once. Archangel fires metal, jagged feathers from his steel wings, though Death smashes them to bits before they can hit him. Below, Cyclops urges Xavier to go get Apocalypse, promising that they can take care of the Horsemen, but stressing they be careful. The Professor has Cable, Beast, and Wolverine accompany him into the passageway. Cyclops guards the door, firing his eyebeams at Pestilence, while Storm darts through the air. Gambit, awfully silent this episode, takes on Famine, flipping away from her horse's hooves, then hurling charged cards at it. Inside the passage, Wolverine takes the lead, and telling the others not to move, he sniffs out what seems to be fresh tree sap. Cable arrogantly claims to know where all the boobytraps are, and presses onward, only to step right into a collapsing section of the path! He manages to grab onto the side of Xavier's hoverchair, keeping from plummeting into the long shaft, with multiple sharp points at the bottom. Beast flips over the hole, grips the ridged ceiling with his flexible toes, grabs Cable, tosses him to the other side, then does the same to the Professor. Logan makes his own way, by clawing into the roof, and jumping over, telling the only non-X-Man of the bunch that maybe next time he'll trust his nose. Thanking him, Cable doesn't understand how he missed that one before, patting Beast on the shoulder for the assist, as he theorizes that Apocalypse will make some alterations in the next 5000 years.
Outside, Archangel is locked in direct physical combat with Death, as they remain in the sandstormed air, before the Horseman finally kicks him off of his grabbing hold of his weapon. Gambit tosses another pair of charged cards, this time at Pestilence, giving her horse a good jolt. Storm directs a tunnel of compressed wind directly at Famine, though she leaps over it with her aerial steed. Cyclops is matched eyebeam to sword-bolt in his battle against War, who finally gives up, and joins his fellow Horsemen as they soar to the near-top of the pyramid. A section is open just for them, and though Death is the last one to enter, just as the door is sliding shut, Archangel is unable to follow, missing it by mere moments. Realizing that the foursome is going back to save the chamber, Cyclops orders his fellow three mutants to head inside, immediately. Inside, the other four mutants reach a crossroads in their journey. Noting how he'll be there in 5000 years, Wolverine asks Cable which way they go now. Before he can answer, the Four Horsemen drop down from the shaft above them, taking them all by surprise, and even knocking Xavier's hoverchair over! Wolverine ends up claw-to-scythe with Death, and Cable plays lasertag with War, before running off down one of the corridors solo. Noticing the mutant's retreat, Logan cuts his fight short by cutting off the top of the Horseman's weapon. It appears that Cable is indeed no coward, as he dives into a passageway, War follows, and once the door behind them nearly closes, he rolls out, leaving the Horseman trapped within! Returning to the crossroads, Cable gloats to Wolverine that he told him he knew where the boobytraps were. As the Professor struggles with his chair, Beast tries to protect him by punching at Pestilence. He manages to make a direct hit on her metal horse, sending her flying off of the steed in defeat. As Beast laments his bruised hand, Famine comes up from behind, preparing to pounce, when the other four X-Men arrive, and blast her back. While Beast helps up Xavier, Death takes flight, escaping the way he came in. Pestilence prepares to do the same, but Cable's excessive laserblasting at her makes her instead decide to swoop through him, knocking the mutant over as the Horseman flees. Wolverine helps him up, and the weary Cable manages to point them to the Lazarus Chamber as being down the corridor to his right. Beast inspects him, finding nothing broken, but won't count on him helping much in the next few minutes. Cyclops says they'll pick Cable up on their way out, and leads the rest of the team to the corridor, intending to find Apocalypse, and do what they came there to do.
Upon reaching the Lazarus Chamber itself, the beam of light cast between the two stone cobra-heads ceases, and the rest of the hieroglyphics and drawings of Apocalypse's persona resume sparkling with power, and the flames throughout reignite. More or less, the "electricity" has come back on in the room, reacting to the presence of the X-Men. Beast is amazed, finding the chamber magnificent, and explaining that the pyramid acts as a huge energy conduct which regenerates Apocalypse while he sleeps. The long stone slab lowers from the ceiling, and unseals the tomb containing the pyramid's progenitor. Apocalypse, his Egyptian body still steaming, is once more exposed for everyone to see. Wolverine sniffs the air, and with his claws drawn, tells them to wait, since he smells two rats in this barn. Xavier concurs, psychically sensing something is wrong. What appears to be Apocalypse from 1200 B.C. awakens, and rises, laughing maniacally, only to suddenly morph into Mystique, equally laughing evilly! She shouts for Apocalypse, and in the Axis of Time, he touches the long control board, as seen in the mirror image Bishop witnesses earlier, causing pinkish energy to crackle about. The Lazarus Chamber is flooded while a blinding light, causing the X-Men to cry out in protest almost all at once. In the crossroads of the pyramid's corridors, Cable notices the light coming from the chamber. He gets back on his feet, and staggers down the hall, calling for Xavier, Wolverine, then Cyclops, and getting no reply. He draws his gun, and once he reaches the chamber, he discovers his teammates in this mission all lying on the floor, unconscious, but alive. Cable screams aloud, wondering what happened. Absent from the scene are Logan and the Professor, not to mention the evil lure. Back at the Axis of Time, Mystique enters the planetoid's dungeon through a portal, and has a sudden, sharp pain in her head. She asks Apocalypse what that was, and he proclaims that it was the most important move of all-- the capture of the king: Professor Charles Xavier! Indeed, now trapped within one of the glass tubes, is Xavier, unconscious, and at the mercy of the manipulator of the ages...