The next morning, Roger Pinkerton, Director of a U.S. government entity known as The Agency, wearily tells receptionist Sympathy Jones that she’s far too inexperienced to be promoted to field agent status. Frustrated that she won’t get a chance to try out her martial arts skills anytime soon, Sympathy laments the fact that she's stuck behind a desk instead of out in the field (EVERY DAY/ SUPER-SECRET AGENT).  That same morning, the impossibly arrogant Nick Steele, a little worse for wear after his encounter with S.C.R.A.T.C.H., limps into the office on crutches.  He is closely followed by fellow spy Henry Greene, who tries to look professional but suffers from a palpable lack of self-confidence.  The two have been summoned for a meeting with Mr. Pinkerton, who puts Henry in charge of the case due to Nick's injury (GET YOUR GUN).  On his way out, Henry stops to talk to Sympathy, whom he clearly has a crush on.  When she appears oblivious to his charms, he gets flustered and rushes out, leaving his confidential case file on Sympathy’s desk.  Soon Sympathy notices the file and, unable to control her curiosity, eagerly reads through it. She decides that she can’t resist such a golden opportunity and resolves to secretly pursue the S.C.R.A.T.C.H. case on her own (SUPER SECRET AGENT REPRISE).

That evening, Richard Oscill's ex-wife Katherine "Kitty" Hawk, the secret leader of S.C.R.A.T.C.H., holds her annual benefit dinner for impoverished children (SERVE THE ORPHANS).  She is aided by her chief henchman/scientist Tick Tock, who also happens to be a disgruntled former employee of Oscillex Labs. But unbeknownst to the benefit attendees, Kitty is actually raising funds for her own nefarious plans, and has her ex-husband tied up in a back room to keep him from interfering. Meanwhile, back at The Agency, Sympathy visits the office of her best friend Caprice Nova, a former Department of Gadgets gofer who has just scored a plush new job in Disguisement.  The two excitedly wade through racks of spy gear to get Sympathy outfitted for her self-assigned surveillance mission (TECHNICAL DISGUISE). And upstairs, in the Agency’s reception area, Henry is desperately searching for his misplaced case file. Mr. Pinkerton enters and catches him rifling through the papers on Sympathy’s desk, but before Henry can muster a decent excuse, Pinkerton informs him that Richard Oscill has disappeared.  After wheedling some much-needed intel from Pinkerton, Henry sets back out into the field with renewed determination (GET YOUR GUN REPRISE).

The Tempo Club is hopping, later that night, as Henry enters to find Ann singing an upbeat go-go number (QUESTION MARK STOMP).  Nick and Caprice are among the dancers, while Sympathy, decked out in her new disguise, sneaks into the background.  Kitty and Tick Tock groove with the crowd for a while and then retire to a table to celebrate their fundraising success. When Ann points out Oscill’s ex-wife, Henry approaches and questions the divorcee about her former husband’s sudden disappearance. He is all business but somewhat lacking in finesse, and the interview is fruitless. Henry exits, and Sympathy, who has surreptitiously planted herself nearby, listens in on Kitty and Tick Tock’s conversation. To her shock, she discovers that Kitty was behind the break-in at Oscillex and plans to use the "time-stopping" technology behind the Delta-29 watch to create a lethal time-freeze weapon. 

In the wee hours of the morning, Nick is dropping off Caprice at the Department of Disguisement following their date at the Tempo Club.  Caprice is hoping to get a jump on some new designs by starting work early, but is still caught up in the haze of her romantic night out. Sympathy rushes in to talk to Caprice about her discovery and is annoyed to find her best friend flirting with the arrogant Nick.  After Nick makes his exit, Sympathy tells Caprice what she’s discovered about Kitty’s diabolical doings.  Caprice is impressed by Sympathy’s sleuthing success, but she’s not pleased to hear that Sympathy intends to go back out and attempt to capture Kitty and Tick Tock single-handedly, insisting that any normal person would be terrified under the circumstances. Sympathy explains that she has just as many fears as anyone else, but she has a special strategy for coping with nerves (PRETEND).

In the wee, wee hours of the morning, Kitty is preparing a bizarrely elaborate death for her ex-husband, whom she has strapped to a giant, clock-shaped torture machine in her penthouse apartment. Before she has time to completely kill Oscill, Henry breaks in and confronts her.  Moments later, Sympathy jumps in through the window and lands in a martial arts pose, both surprising Henry and allowing Kitty the chance to give them both the slip.  After expressing first his confusion and then his anger at Sympathy’s intrusion, Henry asks her to help Richard Oscill get home.  As she is helping him find a cab, Sympathy gently interrogates Oscill and extracts what she thinks could be a key clue as to where Kitty is hiding out.  At the same time, Henry methodically searches Kitty’s apartment for leads, and Tick Tock works feverishly on his time-freeze bomb in the S.C.R.A.T.C.H. lab (FOCUS).

Sympathy returns to the penthouse and excitedly tells Henry that, based on what she learned from Oscill, she believes Kitty’s secret lair is somewhere on Long Island.  Henry is still peeved that Sympathy, whom he has previously known only as a receptionist, is trying to boss him around on his own case. She argues that he doesn’t know what he’s doing, and actually desperately needs her assistance, and the two have a big fight (YOU DON’T HAVE A CLUE).  Just when they are at an impasse, they receive word from the Agency that Kitty has demon-strated her time-freeze bomb on Washington D.C. and is attempting to blackmail the President. Stunned out of their fight by the news, Sympathy and Henry find another piece of vital intelligence that informs them of Kitty’s precise location, and they agree to team up and head for Kitty's hideout together. Meanwhile, Mr. Pinkerton rushes to the White House to advise the President, Agency staff anxiously await orders, and our villains gloat about their imminent victory, each in their own way preparing for what lies ahead (BEFORE IT’S TOO LATE).


Act II

The sun is just rising as Henry and Sympathy emerge from the water—in full scuba gear—and climb up the rocky beach to Kitty’s compound, trying to figure out how to sneak in.  At the same time, in the main chamber of the compound, Kitty waits impatiently while Tick Tock works to build the new, larger-scale version of the time-freeze bomb that they will use to take over the U.S. capitol.  When Kitty inadvertently hurts Tick Tock’s feelings by belittling his contribution to her devious schemes, she must assure him that she values their evil partnership (IF I DIDN’T HAVE YOU).  Sympathy and Henry break into the compound and encounter a series of guards, devious traps, and other obstacles as they race to get to Kitty’s main chamber, learning to depend more on one another in the process (THINK FAST).
Back at Agency headquarters, Caprice is trying to use her skills in design and gadgetry to help make the injured Nick ambulatory again with her special-made “steel wool pants.”  Just as Nick is getting the hang of walking again, Ann shows up at the Agency to give Nick some important intelligence.  Her sources tell her that Kitty has several special bases outside of Washington D.C., and that if those bases are shut down, Kitty will never be able to execute her plan.  Nick is thrilled to finally have some crucial information that he can use to save the day, but as he sets off to do just that...his steel wool pants break.  He implores Caprice to help him, and she promises to fix him up fast (TECHNICAL DISGUISE REPRISE).

It’s noon, and at Kitty’s compound, Tick Tock is setting up the bomb to launch via rocket from a launch pad in the main chamber.  Sympathy and Henry sneak around the edges of the room, assessing the best angle of approach.  They run in and attempt to capture Kitty and Tick Tock, but are foiled, in part because of the swashbuckling moves of Kitty’s personal Swordsman.  Kitty and her S.C.R.A.T.C.H. guards take Sympathy and Henry off to the Alcove of Death, which adjoins the main chamber (HENCHMEN’S MARCH).  There, Sympathy and Henry are chained up and threatened with an elaborate death.  Kitty exits the room, leaving them to their fate. 

Henry eventually figures out how to undo their chains, and frees Sympathy first.  But before Sympathy can return the favor, a guard enters.  Sympathy tries to fight off the guard so that she can undo Henry’s chains but another guard is alerted and she’s forced to run for it.  She scuffles with guards, injures herself in the process, and barely makes it out of the compound, hiding herself in a secluded spot amongst the craggy rocks (I SHOULD HAVE KNOWN).  Scared, she radios The Agency for help.  Mr. Pinkerton orders Sympathy to stay put until a fresh batch of agents arrive, angrily rebutting her suggestion that she go back in to rescue Henry and insisting that would only make things worse. Sympathy, beaten down and disillusioned, contemplates her situation and realizes she has misjudged what it means to be an agent. It turns out it’s much more difficult and much less glamorous than she’d imagined. She decides to quit deceiving herself and face circumstances head-on, and resolves to venture back into the compound to help Henry before it’s too late (A STORY).  She radios Caprice for help, and her best friend convinces Nick he should forego following the lead from Ann and go to help Sympathy and Henry instead. Caprice then consults an Agency blueprint of the compound and, over the radio, guides Sympathy back into the lair through a series of secret passageways; meanwhile Henry struggles to free himself from the Alcove of Death, as he watches Tick Tock’s progress and commits the bomb’s structure to memory (GOT IT).

The sun is setting as Sympathy arrives in the Alcove of Death, where Henry has just finished breaking out of his chains. Together the two burst back into the main chamber to halt the bomb.  As Henry races against time to dismantle it, Kitty and Sympathy face off.  Kitty tries to tempt Sympathy to join her in her evil pursuits (CO-EMPRESS OF THE WORLD), but Sympathy will have none of it and an all-out fight ensues.  Caprice and Nick arrive on the scene and help Sympathy fight off Kitty, Tick Tock, and the S.C.R.A.T.C.H. guards, including the persistent Swordsman. The bomb is de-activated in the nick of time, but Kitty and Tick Tock somehow manage to escape. 

A few months later… Back at Agency HQ, Pinkerton is filling in Nick and Caprice—newly returned from their honeymoon—on the aftermath of the case.  It seems that Kitty has resurfaced in New Zealand and declared herself queen.  Cut to a hotel in New Zealand, where Kitty and Tick Tock are returning from a day at the beach.  As they bicker, we realize that the two attendants behind the desk are Sympathy and Henry, now officially partner agents, in disguise and on the case.  They chase after Kitty and Tick Tock as the rest of the cast emerges from the shadows, singing (FINALE: SYMPATHY JONES, SUPER SECRET AGENT).