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| Mission 3: Senator Rolfe's speech |
| Mission 4: Psilord killed, X-Factor left for dead, Dragon captured by Weapon X program |
| Mission 5: Deadpool & Kane guest app. |
| Mission 6: Wolverine "killed", Dragon brainwashed and sent to attack X-Factor |
| Mission 7: Weapon X storyline continues, SHIELD steps in, X-Factor attacks new Weapon X facility in the Rockies |
| Mission 8: Wolverine regains adamantium, X-Factor escapes |
| Mission 9: "Vacation" in New York, Nate helps out |
| Mission 10: (Feb 8, 1998) Havok, Metatron, and Wildchild join, Nate is captured by the Hellfire Club |
| Mission 11: (Feb 15, 1998) X-Factor ordered to bring back Nate, dead or alive, Blink disappears, Holocaust and Fitzroy attack |
| Mission 12: (Mar 8, 1998) X-Factor stops Hellfire Club, Blink helps Nate escape, against orders |
| Mission 13: (Mar 15, 1998) X-Factor moves to new HQ, Takillya is missing |
| Mission 14: (Mar 22, 1998) Takillya/Nanny/Orphanmaker storyline |
| Mission 15: (Mar 29, 1998)Tak de-aged to 16, X-Factor visits Muir Isle |
| Mission 16: (Apr 5, 1998) Muir Isle, Senator Rolfe reappears |
| Mission 17: (Apr 12, 1998) X-Factor splits, one team returning to HQ, the other disobeying orders and going after Rolfe |
| Mission 18: (May 3, 1998) SHIELD forms new X-Factor, Retro is new recruit, Voltage and Hazard join, Soapman and Metatron return to HQ |
| Mission 19: (May 10, 1998) Darklings attack nearby town, X-Factor returns to HQ, Wolverine taken into gov't custody |
| Mission 20: (Sep 6, 1998) Commander Denning becomes CO of X-Factor, Healer leaves the team, Pegasus and Voltage join, Dragon rejoins |
| Break in logging-- Mission 21: Brotherhood attacks X-Factor, injuring several members badly |
| Mission 22: (Oct 4, 1998) Nightwulf dies, Voltage and Dragon recover from injuries, Hazard is kidnapped by Savior Cyborgs |
| Mission 23: (Oct 11, 1998) Hazard missing, X-Factor is given orders to escort a research team to a top secret space station, guarding against an attack by the Brotherhood |
| Mission 24: (Oct 18, 1998) Brotherhood, disguised as research team, reach the space station and begin wreaking havok, Takillya and Soap-Man are held hostage, Hazard is taken to the same station by mutant researching "scientists" |
| Mission 25: (Nov 1, 1998) Dante, Ripper, and Pegasus further explore the space station, in search of the BoEM, and locate Hazard |
| Mission 26: (Nov 22, 1998) X-Factor, sans Takillya and Soap-Man, flee the exploding space station in their damaged shuttle |
| Mission 27: (Dec 13, 1998) After crashlanding in the North Pacific, X-Factor floats to land, Tak and Soap-Man escape from the BoEM with Shadowcat's help |
| Mission 28: (Dec 20, 1998) X-Factor is reunited at their new base, Frost joins, and Commander Denning is out for some explanations |
| Mission 29: (Jan 3, 1999) X-Factor familiarizes themself with the new base, Cerebro locates Hazard near Washington D.C. |
| Mission 30: (Jan 10, 1999) X-Factor makes the decision to take Mystique and Kerr, against SHIELD orders, and go after Hazard, but Syke reaches him first, and both disappear. |
| Mission 31: (Jan 24, 1999) The team heads back to base, pursued by SHIELD agents, and Crude tags along, apparently coming out of Kerr-induced hynosis. |
| Mission 32: (Jan 31, 1999) A rogue SHIELD agent with ties to a senator defies Fury's orders and continues the attack on X-Factor, Wildchild returns to the team. |
| Mission 33: (Feb 7, 1999) X-Factor waits at base for further developments |
| Mission 34: (Feb 14, 1999) Hazard's biosignature is coming from Las Vegas... Meet Syke. |
| Mission 35: (Feb 21, 1999) Syke places members of X-Factor into a comatose state, and they wake nearly 48 hours later, after Syke has disappeared, and left Hazard with them. |
| Mission 36: (Mar 7, 1999) X-Factor transferred to FBI division, Commander Denning replaced by Commander Smith |
| Mission 37: (Mar 28, 1999) Reports of mutant terrorism in a small European country send X-Factor to investigate |
| Mission 38: (Apr 11, 1999) Ambushed by the Renegades, X-Factor locates the source of the terrorism |
| Mission 39: (Apr 25, 1999) X-Factor is drawn into an astral confrontation with Rift, the leader of the Renegades |
| Mission 40: (May 2, 1999) A vanished town in Kansas prompts several members to investigate on their own |
| Mission 41: (May 23, 1999) X-Factor finds few answers in the deserted town, only discovering ties to the government and more questions |
| Mission 42: (Jun 13, 1999) Returning from the town, X-Factor is attacked at base by a group of strange cyborgs |
| Mission 43: (Jul 18, 1999) The Acolytes strike at the President, but are narrowly thwarted by X-Factor's efforts, along with the aid of two mutants in the crowd |
| Mission 44: (Jul 25, 1999) Exodus and Milan attack the jet as X-Factor attempts to fly the President to safety |
| Mission 45: (Aug 8, 1999) Milan wakes up in the medlab and wigs out, losing control of his powers at the news of Magneto's death, and inadvertently shunting himself into the computer system, as well as causing S.O.P.H.I.A. to develop consciousness |
| Mission 46: (Oct 24, 1999) X-Factor is under investigation about the Presidential incident, and confined to base, when Squadron M, a government-run mutant program, visits for some hands-on training |
| Mission 47: (Nov 7, 1999) Secrets behind Squadron M come out, and Phantasm, Fusion, Commander Smith, and M4 are all casualties of the ensuing fight to get the brainwashed teens to safety at Generation X's headquarters |
| Mission 48: (Nov 14, 1999) After setting up plans with Mace, Gen X's leader, X-Factor returns to the motel to pick up the remaining members of the Squadron, but the government agents in charge have located them, and the motel is blown up during the conflict |
| Mission 49: (Dec 5, 1999) X-Factor is forced to abandon the jet, somewhere in Canada, and set out on foot... and Hazard finds a really big dog |
| Mission 50: (Jan 30, 2000) Enter Sinister |
| Mission 51: (Feb 6, 2000) Enter Sinister, Part Two-- Marauders and more |
| Mission 52: (Feb 13, 2000) Enter Sinister, Part Three-- A new look for X-Factor |
| Mission 53: (Feb 20, 2000) X-Factor visits the old site of Weapon X, where Eve awaits |
| Mission 54: (Mar 12, 2000) Sinister sends Jennifer and the robotic dog after X-Factor to reclaim a teenage boy who slipped onto their jet |
| Mission 55: (Mar 19, 2000) Vancouver BC Night Life, a chance to relax |
| Mission 56: (Apr 9, 2000) An encounter with the Hulk leaves a city block in ruins, Dragon in a coma, and alerts the FBI to X-Factor's presence |
| Mission 57: (Apr 16, 2000) Fun with cows, punks, a new base, and the fellow in the closet |
| Mission 58: (Apr 30, 2000) X-Factor explores the new base more thoroughly |
| Mission 59: (June 18, 2000) The plan to stop the government team is put into motion... and Mystique shows up |
