After a recap of Part 1 Martin and Diana argue about how to escape while Java realizes that when they try to use the malfunctioning watch small openings appear in the energy field. They use this to escape and trap the nearest creatures within the field. Fortunately these aren't the fastest monsters so they're able to flee the chamber ahead of them though enroute they get a look at its viewing pool which shows MOM with the gatekeeper (the hovering evil monk from part 1) and grab MOM's lost amulet.
Fleeing the temple they slide down the mountain pursued by the monsters but fortunately Billy opens a portal ahead of them and they crash into the Center. Later Diana is searching MOM's PC but can't find any info about the Temple though she does learn that before joining the Center MOM drove an ice-cream truck. Diana suspects Billy's holding out on them and he reluctantly opens a portal to MOM's hidden office which holds the top secret Ultimate Legendex. After Java guesses the password they use it to learn that the Gateway temple was created by an ancient order of monks to reduce and contain the amount of evil that can flow into the world. Evil enters through the viewing pool and MOM went there to destroy the pool but was overwhelmed by the power and is allowing evil to flow freely into the world. The amulet she was carrying (which Martin is now wearing) is the key to open and close the Gateway. At which point reports begin arriving of monsters appearing all over the world and overwhelming all available Center agents as global panic spreads. To make matters worse the Legendex says if the Gateway isn't sealed before the sun rises over it (in 3 hours time) the world will be cast into eternal darkness.
If that's not enough then something knocks out most of the Center's power. Martin, Diana, Java and Billy trace the trouble to the detention center where they encounter the Gatekeeper who's out for blood. Fortunately in trying to destroy them he triggers the security forcefields to activate randomly so they're able to escape temporarily. Retreating to MOM's office he traps them but Billy activates a special portal which sucks him in but not before he grabs the amulet.
Before they can relax they meet MOM who has just destroyed the Ultimate Legendex so no one will know how to stop her. She decides to destroy them too but Martin infuriates her enough that she wants to rip him apart with her bare hands rather than use her powers. As she approaches Martin signals Billy to activate a forcefield where she's walking which zaps her back to normal.
The clock is ticking so MOM has Billy transport them to the monster infested city he dumped the Gatekeeper and uses an emergency vehicle she has stashed there to reach the warehouse where the Gatekeeper is waiting surrounded by an army of creatures. MOM orders the gang to stay put and goes to meet the Gatekeeper, as she does she begins looking evil again. Martin refuses to sit idle during the final battle of good and evil and Diana and Java agree to help him back MOM up.
Witnessing evil MOM talking to the Gatekeeper Martin confronts the pair but MOM hasn't changed she was just trying to get close enough to grab the key and since she'd told him she'd destroyed her agents the Gatekeeper figures it out. Working together MOM and Martin get the key and MOM uses her ultra watch to open a portal to the temple but the Gatekeeper follows them.
Back at the warehouse Diana and Java flee back to the van pursued by the monsters. In Tibet the Gatekeeper starts throwing corrosive slime at Martin and MOM so MOM orders Martin to keep him occupied while she fixes things. She enters the temple and uses her watch to solidify the pool. With new evil blocked from entering it's time to seal away the existing monsters which she can do by locking the main gates.
Meanwhile Diana and Java have figured out enough of the van's defenses to slow down the monsters but they're running out of time. MOM uses the key to start the gate closing and the Gatekeeper tries to dissolve her but Martin throws his aim off enough that he destroys the key so there will be no way to reopen the gate. Back at the warehouse the monsters tear open the van and are about to eat Java and Diana when they and all the other monsters worldwide dissolve into red light and head back for the gateway. The lights that were the monsters flow into the gateway which seals behind them except for the gatekeeper who rematerializes but turns to stone.
Back at the Center MOM officially reinstates Martin but announces that since they've just sealed away all the evil in the world the Center has become obsolete so she's shutting down operations and neither she nor Martin will need their watches anymore. MOM intends to return to the ice cream business, Billy is taking a long vacation, Java's off to teach surfing and Martin and Diana return to Torrington to finish their studies. Back at school Diana gets the last laugh when she realizes Martin didn't score a 901 like her but rather a 106 as he held the report upside down. Meanwhile at the deserted Center HQ both MOM and Martin's watches detect an intruder. It's the Gatekeeper and just before the credits roll he begins to laugh as he realizes there's no longer a Center to get in his way.