Speedy, now using the name Red Arrow, slips onto Infinity Island and infiltrates a compound. He finally makes his way to a computer lab where Dr. Serling Roquette is working on a project for her captors, the League of Shadows. Red Arrow subdues her guard and blasts a hole in the wall. She warns that they can’t leave without her project, but Red Arrow tells her that he can only take it or her. Roquette reluctantly goes with him and they make their way to a hidden speedboat. As they leave the island, Red Arrow detonates the explosives charges that he planted on the island, covering their escape. However, Roquette warns that they have one problem.
On Infinity Island, the Shadows’ leader, Sensei, is informed that Roquette left her project behind, and it’s complete.
At Mount Justice, the team hits the beach minus their comrade, Kid Flash. He’s stuck in his first day of sophomore year at Central City High School. By the time he gets to Mount Justice after school lets off, he discovers that Batman and Red Tornado have brought in a new member of the team: Artemis. Green Arrow explains that she’s his new protégé, and his niece. Kid Flash wonders what happened to his old protégé just as Red Arrow arrives via teleporter, bringing Serling with him. He’s angry that his mentor has replaced him so quickly, but Aqualad insists that they’ve always wanted Red Arrow on the team, and still do. Red Arrow explains that he rescued Roquette from the League of Shadows, but they have her project, the Fog. It’s comprised of millions of nanobots which can dismantle buildings and computers, stealing the top-secret data within.
In Miami, Professor Ojo, a League member, unleashes the Fog on a university.
Artemis explains that it’s a typical Shadow operation, prompting Kid Flash to ask who she is. Red Arrow explains that Roquette is working on a virus to render the Fog inert, but the Shadows will try to stop her. He’s hidden her at the local high school computer lab, says that his job is done, and leaves via teleporter.
The team moves into position at Happy Harbor High School, and Miss Martian telepathically links them all together. Kid Flash still blames Artemis for driving Red Arrow off the team, but she insists that it isn’t her fault. She goes to help Miss Martian and Superboy patrol the perimeter, while Robin suggests that Kid Flash cut their new teammate some slack. He points out that she’s the one who secretly helped them against Amazo in Gotham City on their last mission. Meanwhile, Roquette tells Aqualad that she has to go online to track the Fog, but doing so will give away her location. He assures her that they’ll protect her, and she engages the tracking program. Roquette locates the Fog in Philadelphia, where Professor Ojo has it aboard a plane.
In Philadelphia, Professor Ojo detects Roquette’s efforts and notifies Sensei. Sensei sends his closest agents to dispose of the scientist.
As he guards the perimeter, Superboy hears someone in the bushes and starts to investigate. However, Aqualad has Miss Martian reconfigure the bioship so Superboy and Robin can fly to Philadelphia and track down the Fog. As they depart, a Shadows agent, Cheshire, watches from the shadows. She then slips over the fence, going past Artemis and Miss Martian. Kid Flash spots the intruder in the pool area, but she trips him with marbles, knocks him out, and dumps him into the pool. The intruder gets to the computer lab and throws a poisoned shuriken at Roquette, but Aqualad leaps in the way to let it hit him. Aqualad warns Cheshire that his skin is highly resistant and Atlanteans have immunity to poison, and launches a counterattack. Artemis arrives to help her teammate, while Miss Martian rescues Kid Flash from the pool.
Artemis opens fire on Cheshire, who blocks her arrows. However, when Kid Flash and Miss Martian arrive, Cheshire realizes that she’s outnumbered and uses a flash grenade to cover her retreat. Kid Flash blames Artemis for letting the killer past, but Miss Martian points out that she was also on guard. Robin calls to tell them that they’ve arrived in Philadelphia, and Professor Ojo has unleashed the Fog on STAR Labs. They’ve arrived too late: the building is completely destroyed. Aqualad has Roquette rescan for the Fog and moves her to a new location.
The team moves Roquette to a restaurant in town, and Artemis and Kid Flash watch her inside. Two new Shadow agents, Black Spider and Hook, attack Aqualad and knock him out. Cheshire leads them inside and they distract Kid Flash and Artemis while she draws a bead on Roquette. Miss Martian telekinetically block her killing shot, but Cheshire closes in on the scientist… only to discover “Roquette” is Miss Martian in disguise.
Down the block, Aqualad checks on Roquette, who is working at an Internet café as Aqualad guards her. Roquette feeds the coordinates of the next attack to Robin and Superboy, who determine it’s a WayneTech facility. Robin realizes what could happen if the Shadows get access to Batman’s secrets, and that they can’t evacuate the building in time. Below, Professor Ojo unleashes the Fog.
Cheshire orders her agents to keep the team busy while she tracks down Roquette. Artemis tells Kid Flash to take down the others and goes after Cheshire. Cheshire follows Roquette’s trail on infrared, and is satisfied that it is Artemis coming after her. The heroine uses a gas arrow to knock out Cheshire and closes in, but the villainess reveals her mask has gas filters and knocks Artemis out.
Roquette finishes the Fog anti-virus and starts the upload to Robin. Cheshire hits Aqualad with more poisoned darts and knocks him down, then moves in on Roquette.
Superboy spots Ojo and attacks him, but the villain blasts the hero back with an eyebeam and unleashes the Fog. Robin runs into WayneTech, using his knowledge of the security overrides to get past the security barriers.
Miss Martian and Kid Flash defeat Hook and Black Spider.
The Fog tears through WayneTech, and Robin links into the mainframe and uploads Roquette’s attack program.
Cheshire realizes that Roquette has successfully uploaded her program, and her orders are to spare her so the Shadows can make use of her talents in the future.
Roquette’s program deactivates the Fog, saving WayneTech. Outside, Superboy is prepared for Ojo’s second attack, braces himself, and then knocks the villain out.
As Cheshire leaves the café, Artemis fires explosive arrows, knocking her mask off. She recognizes Cheshire, who dares her to let Young Justice interrogate her and find out everything she knows about Artemis. Artemis lets her go and Cheshire slips away into the shadows. Aqualad comes out and Artemis claims that Cheshire escaped. Kid Flash is unimpressed, but Aqualad assures her that their mission succeeded with her help.
Later, Artemis uses a hidden teleporter booth to arrive in an alleyway in Gotham City. Red Arrow is waiting for her, and says that they both know she’s not Green Arrow’s niece. He figures that his former mentor and Batman have a reason for lying, but warns her not to hurt his friends.
Sensei reports to the Light’s Board of Directors, and informs them that they didn’t get the WayneTech intel that they needed. The Board is satisfied with their progress, since they have an infiltrator within Young Justice.