Three experienced B-Squad cadets, Sky, Bridge, and Syd, are assigned to bring in a pair of criminals who, just like them, possess genetic powers. Before they begin the capture, they are promoted and given Delta Morphers, becoming Rangers Blue (Sky, much to his dissatisfaction; he has wanted to be the Red Ranger like his father), Green (Bridge) and Pink (Sydney) when they perform their first morph in Part 2.

Kids mock a lonely boy named Sam for his teleportation abilities. He becomes a target for Mora, who promises to be his friend if he helps her creation Bugglesworth turn the city's population into dolls. When the Rangers confront Sam, Z tries to befriend him, but he refuses. When they find out the captives will be trapped permanently in doll form soon, Z and Jack find Sam and try to convince him that being different isn't a bad thing. However, Bugglesworth appears and convinces Sam to come with him while leaving Jack and Z to deal with a new, extremely powerful Orangehead Krybot.

Doggie is plagued by nightmares involving his home planet Sirius, and Emperor Gruumm is plagued on how to defeat the Rangers. Still, Mora gives him advice to beat someone by taking out their leader. To stir up trouble, Gruumm visits Earth and takes a human form to visit Broodwing at Piggy's new restaurant, which he formed from the money that he won from a discarded winning lottery ticket. Kat discovers a strange energy disturbance caused by Gruumm's visiting General Benagg, an old "friend" of Commander Cruger, causing Cruger's pain only to worsen. Benaag calls Cruger out to battle, but Doggie still refuses, revealing to the Rangers the history of Sirius and the origins of S.P.D. Meanwhile, Kat is ambushed by Krybots outside the base and confronted by Benaag after Cruger angrily orders her out of his sight.

The B-Squad finds a standout D-Squad cadet in a girl named S.O.P.H.I.E. (Series One Processor/Hyper Intelligent Ecryptor), who succeeds where her fellow D-Squad members failed by defeating Krybots during a training exercise. Mora begs Gruumm for one last chance to defeat the Rangers to keep her childhood and recruits Valko to assist her. Valko reveals his plan to defeat the Rangers by attempting the impossible: gaining control of a massive robot named Goradon. But first, he needs a piece of technology that only S.P.D has, and S.O.P.H.I.E. matches his needs through her body having something he is after. Meanwhile, the new standout cadet takes matters into her own hands to help out when Kat needs to decrypt a new sequence for phase 2 of the base's Delta Base Defense System (D.B.D.S.). The first phase of the D.B.D.S. sees the base morph into a Delta Command Crawler mode that moves the base into battle. However, after the battle, S.O.P.H.I.E. is discovered to be a cyborg, having kept it a secret out of fear of being expelled for not being human. When she is interrogated about trying to access the D.B.D.S., the Rangers - including Bridge, who saw her potential as a cadet - distrust her and she is subsequently expelled.

Boom gathers everyone for an urgent update from his makeshift radio signal grabber he built. A message comes through from the future, telling of S.P.D.'s defeat at the hands of the Troobain army in the year 2040. While discussing whether they should believe the news or not, Morgana puts her plan into action, taking time to torment Z who hurt her doll in "Sam: Part 1". Things get even worse when the prophecy seems to come true with the aid of Morgana's most powerful allies, the brothers Shorty and Devastation. Birdie gets back to them upon receiving the news and states that he can't send any help to them as he fears sending reinforcements might be falling into a trap by Gruum.

The B-Squad's day off is brought to a halt when criminals they've already contained attack New Tech City, leaving them perplexed as to how they could've escaped. Upon finding out the criminals are still in containment, Kat borrows Jack's morpher to upload the S.P.D. Battlizer, much to Sky's continued lament about not being the Red Ranger. Later, Sky travels to Gamma Orion and visits Mirloc, a criminal locked in a specially-made cell due to his ability to travel through reflective surfaces, to gather information. Thanks to Sky, the Rangers confront the real culprit: Slate, a copycat criminal whose powers allow him to mimic anyone. Morgana joins Slate and infuses him with a special formula that transforms him, in a divide-and-conquer-like transformation, into all of his impersonations of the criminals the Rangers successfully defeated so far, and Jack calls for his new Battlizer to defeat Slate's mutation into a criminal split in a team of impersonations. In exchange for the info Sky received, Mirloc wants to know what Sky's saddest memory is, and Sky tells the story of his father, who was the Red Ranger years ago, and was slain in battle. Mirloc mocks Sky's story, and the upset Sky sheds a tear. Mirloc takes this opportunity to travel into Sky's tear and escape his cell, leaving Sky stunned as he realizes what has happened.

The Rangers are constantly fighting with each other, hindering their team efforts when an S.O.S. message warning Cruger and Kat of a horrible upcoming threat puts them on edge and Kat in a rush to finish some updates. However, Kat accidentally destroys her quantum enhancer in her haste, and Z goes to Piggy to get a new one. What they don't know is Gruumm has put a time limit on Piggy to stop S.P.D., and he takes the chance to give them a new one with a virus inside that Thresher and Stench, Piggy's acquaintances/customers, use to get into S.P.D. files. With Thresher causing a distraction, Stench can download the schematics for the Rangers new S.W.A.T. (Special Weapons And Tactics) mode. When the Rangers constant bickering causes the criminals to get away, Commander Cruger sends the B-Squad to Planet Zentor where they are trained under the watchful eye of Sergeant Silverback. The irate Sergeant and his bulldog-modlede R.I.C. quickly put the Rangers through their paces, pitting them against reprogramed Krybots and a giant scorpion monster.

With help from his associate Professor Cerebros, Broodwing uses the Red, Blue, and Yellow Dino Gems to transport Conner, Ethan, and Kira to 2025 as part of his plan to defeat the Rangers and destroy the planet. The three confused Dino Rangers escape with their Gems and are soon cornered by Krybots, only to be saved by the B-Squad and taken back to the Delta Base. Although Doggie insists they remain at the base to avoid disrupting the timeline, the Dino Thunder Rangers decide to do what they feel is right, teaming up with the B-Squad to drive back a robotic army and the Dragoul creature.

Gruumm decides to take drastic measures to stop the Rangers by traveling through a wormhole 21 years into the past where S.P.D. doesn't exist. Upon realizing what Gruumm has done, the B-Squad pursues him to the year 2004 and meets up with the Dino Thunder Rangers again. Meanwhile, Gruumm forces Zeltrax to join his army and ultimately faces the combined might of twelve Rangers who are determined to save the past, present, and future.

Guest Stars: James Napier, Kevin Duhaney, Emma Lahana, and Jeffery Parazzo.

The traitorous A-Squad capture Commander Cruger and call out the B-Squad, who meet their counterparts for an intense battle. Meanwhile, Broodwing makes his final push for domination and gathers an army to attack the Delta Base while the Rangers are away. The B-Squad fights the A-Squad, losing the Delta Squad Megazord in the process. However, thanks to S.W.A.T Mode and the S.W.A.T. Megazord, B-Squad wins and captures the traitorous A-Squad. Then, the Rangers break into the Delta Base and contain Broodwing and his allies. Unfortunately, they still have to deal with Gruumm, who catches them with help from Piggy.