Diego de la Vega, the son of a wealthy landowner, returns from his studies in Spain and discovers that Los Angeles is under the command of Capitan Monastario, a cruel man who relishes in the misuse of his power for personal gain. Knowing that he cannot hope to single-handedly defeat Monastario and his troops, Diego resorts to subterfuge. He adopts the secret identity of Zorro, a sinister figure dressed in black, and rides to fight Monastario's injustice.
The second season of Zorro opens with Don Diego and Bernardo visiting Monterey, California. They have been sent there by a group of Los Angeles investors to look over an import business. The visitors have barely arrived in town when two men burst into their room and demand the investors' money.
Diego continues his investigation into Señor Verdugo's business by riding to his house, where Verdugo greets him and Bernardo with his arm in a sling. Although Verdugo claims an old injury is bothering him, Diego suspects he may be the leader of the robbers, so he sets a trap.
Lieutenant Rafael Santos is ambushed on his way to Monterey and left for dead when the ambushers take his identification and uniform. One of them, a killer named Anastacio, puts on the uniform and rides to Verdugo's, where Diego is discussing the investment deal.
After the Verdugos return to Monterey, Anna Maria enters their home and discovers that her father is missing. Pablo, their former servant, tells her the old man is being held hostage and will be killed unless she hands over 45,000 pesos believed to be in the house.
The kidnappers send word that Anna Maria must meet them if she wants proof her father is still alive, but Diego warns her it is a trick. Romero argues that she must go, so she agrees to go with him, Garcia and Reyes.
Before he returns home, Sergeant Garcia angers Theresa, a tamale vendor, when he tries to carry out the orders of the acting governor. Luis Rico has decided that all of the vendors must be removed from the plaza despite their objections, and Diego promises Theresa he will try to help.
Joaquin and several followers begin a series of raids against the Especials, which culminates with the beating of Capitan Briones. The soldier issues a death order for Joaquin and sends his men after Theresa, intending to force her to reveal his hiding place. She asks Diego to hide her, and with Garcia's assistance, he protects her from the searchers.
Capitan Briones escalates his campaign against Joaquin by ordering that a peon be whipped until he reveals the rebel's hiding place. Zorro uses his own whip to stop Briones, then frees the peon. Shortly after, the real governor returns and Rico explains that his harsh rule was only imposed to make the capital a well-run city. Rico then convinces the governor to offer the rebel a truce so he can explain his case, planning all the while to kill Joaquin as soon as the outlaw turns himself in.
The broken truce has convinced Joaquin that Diego cannot be trusted and, that if not for Zorro, he would have been killed. When Diego and Bernardo ride to his camp to explain, the rebel leader orders his men to lock the visitors in leg irons until he can decide upon a suitable fate for them. Joaquin announces his plans to kill the governor the next day while he visits a local shrine. When he tries to ride there, however, Joaquin is accidentally captured by Sergeant Garcia.
Anna Maria Verdugo returns to Monterey from San Francisco and becomes the object of Ricardo del Amo's affection. This friend of Diego's is an incurable practical joker. Ricardo realizes that Diego is also attracted to Anna Maria and hopes to lessen the competition by having some fun at his friend's expense.
Ricardo asks for Diego's help in winning Anna Maria's heart, for he feels Zorro is too much competition for the two men to overcome. If they can make it seem that Zorro is seeing another woman, Anna Maria will scorn him, thus dropping the field of suitors to a more manageable size. Ricardo plans to accomplish this by dressing as Zorro and serenading Anna Maria's cousin, Milana del Carmen.
Diego doesn't know that Ricardo has developed a hatred for Zorro. He makes matters worse when he substitutes a block of wood for a box of chocolates intended for Anna Maria. When she opens her present and Ricardo sees the wood, complete with a carved "Z", he decides to kill his unmask his foe.
Ricardo leaves town but causes another problem for Diego before he goes. Still infatuated with Anna Maria, Ricardo tells her that Zorro would unmask himself if he really loved her. The problem is, Diego does love her, and thus begins to consider turning himself in. The governor offers the outlaw amnesty if he will surrender himself at a public ceremony.
Two indentured servants who wish to marry find that the law states they must have the permission of their masters. Buena, who works in the de la Vega hacienda, is told she is free to marry, but her boyfriend, Romaldo, is not so fortunate. One of his co-workers also wants to marry Buena so he convinces their boss that Romaldo plans to run away after the ceremony.
It is time to send the tax money to the governor, and Sergeant Garcia has a plan to thwart any attempt to steal the funds during the long journey. He orders the town blacksmith to build a huge iron box that requires a special key to open it. The money will be placed in the box and the key sent to the governor by a separate route.
Diego's uncle, Estevan de la Cruz, arrives in Los Angeles for an unannounced visit and surprises the de la Vegas when he tells them he plans to be their house guest. Furthermore, he expects them to give a lavish party to welcome him. All of this angers Don Alejandro, but to head off a family dispute, Diego convinces his father that Estevan will leave soon.
Estevan again becomes a problem for Diego when he decides to earn some easy money. Los Angeles is preparing for its annual horse race and Estevan would like to win the prize money, but his horse seems unlikely to win. His luck changes when he comes across Zorro's horse, Tornado, grazing in a hidden field, and he captures the animal.
Still hoping to strike it rich during his visit to Los Angeles, Estevan shows a great deal of interest in a young woman when he learns she comes from a wealthy family. Don Alejandro accuses Estevan of only being attracted to Margarita because of her money, but the suitor denies the charges, forcing Diego to dress as Zorro in an attempt to frighten Estevan away.
Estevan still hopes to marry the wealthy Margarita but he knows that Zorro will continue to oppose him. Don Alejandro suggests that if Estevan were to settle down and begin farming, Zorro would realize that his intentions are honorable. He gives the visitor a small plot of land and wishes him well in his endeavor.
Los Angeles is suffering from a severe drought and tempers are fraying as crops and animals die from the lack of water. Most of the landowners are helping their neighbors by allowing them access to the few wells and springs that have not yet dried up.
A mystery develops when a teenage girl arrives in the pueblo and asks for directions to a ranch no one has ever heard of. Anita Cabrillo has been studying at a boarding school, and she has come to visit her father, whom she has not seen in many years.
Anita is still hoping to find her father, but Sergeant Garcia has decided she is nothing but a liar and wants to send her back to Spain. Only Diego believes her story, and he tells her she needs to supply some proof of her father's existence.
Don Alejandro remains firm in his wish to send Anita back to Spain and tells the girl to pack her bags. Gonzales arrives to take her to the ship and Anita gives Alejandro a goodbye kiss.
When a jovial mountain man, Joe Crane, arrives in the pueblo, he is threatened with arrest for traveling in Spanish territory without official permission. Sergeant Garcia warns him to leave town but changes his mind when Crane buys him a few drinks in the tavern.
Thought to be hiding safely in the hills, fugitive Joe Crane instead has sneaked back into the pueblo hoping to recover his hunting rifle and the load of furs he gathered during the trapping season. He also wants to see Carlotta, the barmaid who accidentally started the fight between him and Don Carlos Fernandez.
Don Carlos Fernandez decides to draw Joe Crane into the open by laying claim to the mountain man's furs and burro. Diego tries to end the feud by offering to buy the goods, but Fernandez refuses.
Basilio has begun to enjoy his stay in Los Angeles despite Zorro's interference. He is surprised at how well his war bonds are selling, for the landowners have decided to help support the Spanish government as much as possible.
Even with his stolen gold gone, Basilio plans to remain in Los Angeles as a wealthy man. He decides to do so in a way that will let him exert a hold over Moneta Esperon, the attractive daughter of a wealthy landowner.
Humiliated by Zorro, Basilio gets his revenge by arresting Sergeant Garcia and hoisting him in the air in the public square outside the cuartel. A large sign dares Zorro to rescue Garcia, but Diego knows Basilio will have hidden lancers throughout the area. When night arrives, so does Zorro, using Bernardo to help create a diversion that draws the soldiers out of town.
Pedro Avila, recently arrived in the pueblo, earns a meager living by betting other men that he can beat them in a sword fight. He tries to talk Diego into betting, but Diego refuse, as Diego knows he must keep his skill a secret. This gives Avila and his friend Tony Pineda an idea about how to get rich. They plan to force Diego into a duel, then allow the frightened man to buy his way out of the situation.
Sergeant Garcia returns from escorting Padre Simeon on a trip from San Diego and is surprised to find that almost everyone in Los Angeles has contracted the measles. The doctor has placed the entire pueblo under quarantine and restricted residents to their homes. Even the soldiers cannot leave the cuartel.
The governor of California is attacked during a visit to Los Angeles with his daughter and aide, and barely escapes with his life. Taken to the de la Vega house to recover, he is much too weak to travel for several days. The aide, Capitan Arrellanos, tells Diego he suspects the attack to be the work of the Rebatos, a group that wants to sever ties with the government in Spain.
Capitan Arrellanos refuses to help the Rebatos any longer in their attempts to kill the governor. Instead, he chooses another plan designed to make him the head of the government. He asks the governor's daughter to declare her father too ill to continue in office. Furious at this request, Leonar refuses to cooperate. She then tells her father of the aide's plot.
Capitan Arrellanos continues his attempts to rule California by hiring Carmelo, a recent arrival to the pueblo, to kill the governor. Diego and Bernardo overhear the plan but don't act at once, hoping instead to learn who the other conspirators are. The governor has begun to recover and spends his time sitting outside on the patio, which prompts Don Alejandro to give a party to celebrate his better health.
The recovering governor is beginning to become irritated by his confinement to the de la Vega home. At times it seems as if the only thing that can pacify him is a music box. Almost as soon as it begins to play, the governor falls asleep. Knowing that the Rebatos are still trying to kill the governor, Diego uses the box to lull him to sleep then Bernardo moves him to safety.
Don Sebastian, a friend of the de la Vegas, is growing impatient at the delay of the stage to Monterey, for he is carrying a purse full of gold and is afraid it may be stolen. While waiting in the tavern with Diego, he makes the mistake of mentioning the gold and is overheard by three crooked entertainers.
A Chinese boy escapes from a ship in San Pedro's harbor and tries to hide in Los Angeles. He is unable to seek help, for he speaks only his native language.
Celesta Villagrana and her servant, Montez, are on their way to Los Angeles when a hooded robber stops them and steals her jewelry. The thief knocks the travelers to the ground then departs, leaving Celesta lying there unconscious.