Mrs. X breaks her leg. To solve this problem, Truman builds a replacement. However, this does not seem to work well.
SUPERIOR decides to take Mr. and Mrs. X out of their ranks as punishment for destroying Stonehenge, as they have Home Base place Truman and Tuesday in command instead.
Mrs. X arranges a slumber party for Tuesday; during it, the family begins to fight Glowface. Tuesday tries to cover up the truth about her family.
Truman's unauthorized upgrade of Home Base forces the computer offline for a day. They try to work to get all the household chores done before an inspector from SUPERIOR shows up. If anything is out of place, the X's will be sent to a foreign country to herd farting goats.
The X's get a family portrait taken in order to try to blend in as a normal family. Unfortunately, this turns out to be an ambush by S.N.A.F.U. as Glowface leads Lorenzo Suave, Sasquatch, the Scream Queens, the McVampires, Bio-Harold, Missing Link, and Some Old Guy into attacking the X's.
After missing every birthday celebration because of world-saving missions, Truman gets a puppy for his birthday and names it "Rex", but it turns out it is from Sasquatch, who has amassed an animal army.
In his effort to pass for a normal dad, Mr. X learns that normal dads fix things, so he begins to do that. Of course, he's terrible at it.
Truman and Tuesday are forced to share a room, after Truman's room accidentally goes nuclear.
Mrs. X and the kids trick Mr. X into giving them stuff they want, by rewriting his official spy manual with the Retextinator to include the items they desire.
Tuesday's first date is with a guy named Brandon who is too good to be true: in fact, he is a spy working undercover for his uncle Glowface.
Truman attempts to be good and refrain from pulling pranks for one entire day, so he may join his family at the "world's greatest" amusement park.
Mrs. X is filled with peace and tranquility, after she returns from a retreat. Unfortunately, these qualities prove useless when confronting Glowface.
Mr. X gets a job as a mailman. Meanwhile, Sasquatch works to breed the ultimate dog.
Tuesday wants the family to learn how to bowl. Their lessons get crashed by Glowface, Lorenzo Suave, Sasquatch, and Brandon who were annoyed that they are bowling when not trying to stop their heists.
A girl at school picks on Truman, but he finds out it is because she has a crush on him.
Mr. X has a dirty little secret that is locking him away from being a spy and hanging with his family, but what could it be?
The entire family gets sick, except for Tuesday. The same thing happens at S.N.A.F.U. HQ where Glowface, Sasquatch, and the Scream Queens get sick, leaving Lorenzo Suave to care for them. Seeing this as an opportunity to do one of his plots, Lorenzo begins his plot for world conquest, which attracts Tuesday's attention.
Mr. and Mrs. X go on a romantic date, but while they are away, Tuesday and Truman throw a party. Glowface seizes the opportunity to attack Home Base.
Truman and Tuesday are failing their cooking and tennis classes (Tuesday with cooking; Truman with tennis). They'll be forced to go to summer school if they fail their test. So their parents try to help them with those subjects. Mrs. X helps Tuesday and Mr. X helps Truman; the only problem is that Mrs. X, who is a good tennis player, turns out to be a terrible cook while Mr. X, who is a good cook, turns out to be a terrible tennis player!
Truman finds the perfect opportunity to drive Tuesday crazy, when she gets braces. He interferes with her braces to make Tuesday say crazy things, while she is on her date with Brandon.
In their continuous effort to be like "normal families", the X's visit a family counselor to see what kind of issues "normal families" have. However, it is not long before they start to take their "roles" too seriously.
Truman gets a chance to capture the most wanted villain which is Copperhead. The rest of the family begin to suck up to Truman to capture Copperhead with him.
When the X's win a billion dollars, they must balance their new fame and fortune with their spy work.
Sick and tired of being short, Truman builds a small replica of Home Base for him to live in, until he misses his family.
When the X's punish Truman for hotdogging a mission and blowing up the X jet by selling all of his spy gadgets, Glowface persuades the boy to join S.N.A.F.U., his first mission: destroy the X's.
Truman has a crush on Tuesday's friend Kimla. Truman realizes there's only one way to get past this "little kid" thing – he has to tell her he's really an international super spy. Not surprisingly, Kimla doesn't believe him. Surprisingly, she continues to disbelieve his story even when he sneaks her along on a mission and the truth is right in front of her nose.
The archenemies of the X's, the Y's, move in next door. The X's suspect they are up to no good, but cannot prove anything until the Y's show their true colors during Glowface's next plot.
When Tuesday is suspicious of Brandon, the X's find out that he is a part-time S.N.A.F.U. agent.
Home Base explodes, when the X's forget his birthday. Without Home Base, the X's need to survive on their own.
The X's have to babysit a neighbor's baby, and they cannot change his diaper. Will they ever be able to change that diaper?
The X's try to prevent Mrs. X's parents from realizing that they are spies when they come for a visit.
After the X's go on a mission, Truman faces an ultimatum where he has a single day to train Rex, or else he will go to the pound.
Truman creates a body for Home Base so he can carry the X's weapons, but the X's hate it. It even gives Home Base problems when he tries to stop Sasquatch, Bio-Harold, and the Scream Queens alone.
Truman attempts to scare his family by turning Home Base into a haunted house, but Glowface takes control of the Home Base, and soon, Tuesday, Mr. X, and Mrs. X are zombies. Can Truman stop Glowface's evil plot before his brain is eaten?
Truman saves a baby from one of his paintball traps, and the public hail him as a hero; Tuesday tries to expose Truman as the culprit.
After Mr. X's necktie reflects off Glowface's base walls, he suffers a tie loss. He now cannot fight. Can the other X's save Mr. X from his loss of "Mr. Tie-tie", or will the X's become nothing?
Brandon will play Romeo in the school play of Romeo and Juliet, and Seven Y competes with Tuesday to see who may play Juliet.
Mr. X takes Truman to his favorite childhood camp, hoping he will love it, too. Turns out Truman does not, much to Mr. X's dismay.
