After the battle with the Overlord, the Ninja, Kai, Jay, Zane, and Cole now teach at Master Wu's Academy.
While Kai was showing his students the events and the aftermath, a small film with Jay filming him singing in the shower soon came on, infuriating him and stops the film before a student comes in, saying Zane is on the fritz.
At Zane's class, Brad uses a remote he got from New Ninjago City to control the Ninja of Ice and only thanks to Cole was he freed. During recess, the Ninja and Master Wu take a break.
"Lloyd's lucky getting to fly around receiving awards while we're stuck here" Kai complained as he gave Jay his pudding cup
"Any signs of Aria lately?" Cole asked
"None" Zane said
"She's still missing?" Jay asked
"Yeah" Cole said sadly
"Lloyd doesn't even know, the kid would go crazy knowing she's missing" Kai said
"They're in denial of their own feelings~" Jay sang
"What?" Zane questioned
"He's saying Lloyd's got the hots for Aria" Kai said
"...what?" Zane asked still confused
"They mean that Lloyd likes Aria, likes likes her" Cole said
"It's quite noticeable" Zane said finally understanding
They are interrupted by Nya coming in "Guys news!"
"What danger?" "A new villain?" The ninja asked excitedly
"No we goy clearance for a field trip to Borg Industries, Borg Tower" Nya said excited and the ninjas all groaned
All the students and teachers of the academy take a bus to New Ninjago City, which has been rebuilt and upgraded in the wake of the battle with the Overlord through the efforts of Borg Industries, headed by inventor Cyrus Borg.
Distracted by the incredible new technology, Nya accidentally crashes the bus straight into the Postman's hover truck.
Cole exits the bus to extricate it from the crash, but a Borg Industries Security Mech arrives and asks him to move aside as it deals with the problem.
Master Wu decides that since they were a short distance away, the pupils and teachers should take the walk to the building by foot. Entering the tower, the visitors (except for Kai, who gets stuck in the door) are welcomed by P.I.X.A.L.
She's a female android created to act as Borg's assistant. P.I.X.A.L. is especially fascinated by Zane, and scans his inner-workings under the Nindroid's permission.
She then notifies the Ninja that Cyrus Borg is waiting for them on the 100th floor in his office, and then leads the students, Master, and Nya for a tour of the tower and its technology.
Sally then encourages Nya to try out the Perfect Match Console, which reveals her perfect match to be Cole.
As the Ninja arrive in the office of Cyrus Borg, the Ninja were all very happy to meet him.
"No Gold ninja? Overlord's daughter?" Cyrus asked
"No Lloyd's busy" Cole said
"Aria's a part of the team now, so please stop calling her the Overlord's daughter, and not her either, she's missing" Jay said a little angry
Cyrus, after letting the them look around, shows them to a gift he wanted to give them: an automated statue of himself.
It looked like a regular statue, but Cyrus whispers to Kai that they should protect "them" with their lives and to not let anyone know they had them.
He then tells them that they must leave since he has things to do. Walking into the elevator with their gift, they begin to get suspicous about Borg.
Being distracted, they accidentaly drop the statue, yet they discover it is hollow and is filled with new suits as well as the Techno Blades.
Suddenly, a robotic security voice in the elevator says that they should drop the blades. The Ninja refuse, and the elevator drops toward the ground at high speed.
The Ninja luckily escape into an elevator going up right next to it, and manage to get their new outfits on for battle in their escape from Borg Tower.
In the meantime, P.I.X.A.L. leads Wu, Nya, and their students to the factory area, in the moment system being hacked so she also gets under control of it, saying that this will be the end of their tour.
When Ninja get out of the elevator, they get attacked by Security Mechs. They try to fight them with the Techno Blades, but don't know how to activate them and realizes that's not way they work.
A Mech fires their rocket to the glass, breaking the window and pushing the Ninja out. However, they survive after grabbing onto a hanging hose and hitting a window cleaning platform.
On the platform, they get attacked by enemy copter but before it manages to fire at them, Zane jumps on it and hacks it with his Techno Blade, finding out that's the way how the said "weapons" work.
In Borg's office, the inventor attempts to explain himself to the Digital Overlord. His efforts prove fruitless however, as the Overlord assimilates him into a drone.
"I want my daughter!" He shouted
In the factory area, machines invade students and P.I.X.A.L. starts chasing them, but they find the exit to the outside. There they get picked up by Zane's new vehicle leaving P.I.X.A.L. because Nya realizes she's one of "them."
When they get down of the tower, Master Wu takes the Techno Blades and says that he wants Kai and Zane in the air, and Jay and Cole on the ground.
Cole manages to defeat the Security Mech and hacks it with his Techno Blade, making it the Earth Mech. Jay invades a tank and hacks it, making it the Thunder Raider.
Kai jumps on Zane's copter and hacks an enemy airplane, making it the Kai Fighter and reaching outer space. While he was flying, Cyrus Borg gives him a virtual message saying that few weeks ago they discovered that a virus, the Digital Overlord, had infiltrated their system.
He also says that they have to get the Techno Blades out of the city, because if he finds out that they have them, he will never let them leave. And one more thing, the Overlord is wanting to get his hands on Aria.
After that, Kai lands to pick up Wu, but they get surrounded with Security Mechs. At the last moment, Lloyd arrives on the Golden Dragon, defeating the robots.
At the same time, the Overlord appears on the screens around them.
"I defeated you once and I'll defeat you again" Lloyd said
The Overlord laughs and says "I just want your power"
The overlord stops laughing and looks at them and growls "where is my daughter!"
Lloyd then looks around as well, now realizing that Aria is not there.
As the Ninja get back into the vehicles and race to leave the city, Overlord spots that Wu is getting away with the Techno Blades so he sends two copters which capture him on a building rooftop.
However, upon rewinding the footage, the Overlord sees that Wu quickly dropped Techno Blades into Kai's Fighter below him.
The Ninja safely got out of the city with the blades, while Wu is captured by Overlord's forces.
"We have to go back for him" Lloyd says
"We will, but only when you are safe" Kai said
"He wants these weapons and for some reason he also wants you" Cole said
"And Aria" Jay added
"Remember this is sensei's plan, they can't break him" Cole said
"Yesterday is gone and tomorrow is yet to come, we need to worry about today" Zane repeated sensei's words
Jay sighed "you said it Zane"
"We will come back to new ninjago city and when we do we will be ready" Zane said
"But for now we find somewhere safe to hide, they'll be looking for us" Kai said
"And we need to find Aria before they do" Jay added
"That's right, they'll be looking for her" Kai said
As the sun rises over New Ninjago City, The Digital Overlord takes control of Cyrus Borg while P.I.X.A.L. begins a massive production of Nindroids using Zane's scans.