It must have been an eye-opening experience to watch Missy Elliott’s performance at the MTV video music awards last month if you had never encountered her before. Her six-song medley was a thrill-ride of kaleidoscopic visuals, VMAdancers and costume changes: Elliott was a cyberqueen, a B-girl, a scarecrow, an airborne beachball, a one-woman advertisement for what pop music can be. The performance, marking her video vanguard award, instantly went viral, capped a year of honours (an honorary doctorate from Berklee College of Music, the first female rapper in the Songwriters Hall of Fame) and coincided with the Iconology EP, her first new body of work since 2005. It dazzled the uninitiated while reminding millions of older fans what a vital creative force the 48-year-old was and how much we had missed her.

Two days later, Elliott is still bathing in goodwill. “It’s a blessing,” she says, calling from New York. “A blessing!” She has a throaty southern accent and a brilliant, exclamatory laugh. After a month of planning and two weeks of rehearsals, she says the set went like a dream. “The only time I was scared was when I was backstage and I had to keep changing clothes really fast. I thought: ‘Oh God, I’m not going to have my pants on in time. I might be in my panties!’ Ha ha!”

Katy Perry and Missy Elliott perform at Super Bowl Halftime in 2015. Photograph: Christopher Polk/Getty

This is not Elliott’s first comeback but it feels different. The last time she returned to the public eye, as Katy Perry’s guest during the Super Bowl half-time show in 2015, she “freaked out” the night before, daunted by the size of the audience and the length of time she had been away. “I ended up in the hospital for having an anxiety attack,” she says. “I think any artist who has had a break such as that one would be anxious. I remember Katy saying: ‘This is the perfect time to perform your new record. It’s the biggest platform.’ I was like: ‘I don’t even know if they remember the old ones so I most definitely don’t want to do a new one!’ I’m always anxious whenever I drop anything because you just never know if they’re going to get it. So I’m always biting my nails and pacing the floor.”

Elliott was meant to release her long-overdue seventh album that year but after just one brilliant single, WTF (Where They From), she returned to her quieter life as a writer, producer and guest MC. “I hate to say I’m back because in reality I never went nowhere,” she insists. “I was still doing stuff behind the scenes. I don’t always want to be upfront. I’m very shy.” I suggest that anyone watching her fly through the air in an inflatable leather suit at the VMAs would not automatically diagnose her with shyness. “I was like that as a child,” she says. “We would have family reunions and they always wanted me to get up on the table to perform. After an hour of them begging me, I would finally get on the table and become this other little kid. Then they couldn’t get me off. Once I set foot on the stage, I block out everything. I can be in my own world.”

Melissa Elliott first constructed a private world as a child in Virginia. It was a fantastical refuge from a violent father, an abusive cousin and the grind of poverty; when reality fails you, build your own. Behind her bedroom door, she was a star, practising acceptance speeches in the mirror and performing to an audience of dolls. “The teacher would ask what everyone wanted to be and I said: ‘I’m going to be a superstar.’ And everyone in the class would laugh. I wonder if those kids remember me to this day, because I remember everyone.”

In high school, Elliott formed an R&B group called Fayze, who later signed with the Swing Mob label under the name Sista and moved to New York. But Sista flopped and the Swing Mob crew dissolved, so Elliott didn’t hit her stride until she returned to her home state in 1995 with her best friend and producer Tim “Timbaland” Mosley. “Timbaland was more quiet than me and I’m super-shy so just imagine,” she says. “He’s most definitely not like that now! Through him I met Pharrell and we all bonded.”

Missy Elliott and producer Timbaland in 2004. Photograph: Jon Furniss/WireImage

Avoiding the radio and MTV, the Virginians tunnelled deep into their imaginations to find genuinely new sounds. Elliott describes one memorable day in Virginia Beach’s Master Sound studio: “I was in the booth doing The Rain [her debut solo single] and I kept hearing: ‘I hate you so much right now!’ And I was like: ‘Yo, who is screaming?’ I’m getting so mad. And Pharrell comes knocking on the door and says: ‘I want you to hear something.’ And he plays it and it’s Kelis. Me and Tim were like: ‘Man, we wish we had done that record.’ That’s how we pushed each other.”

Missy “Misdemeanor” Elliott could do it all – sing, rap, write, produce – but what she and Timbaland were doing was so far out that they needed to prove themselves, first by working on Aaliyah’s 1996 album One in a Million. It was the shape of R&B to come: radical yet irresistible. For her own The Rain (Supa Dupa Fly), Elliott cooked up a joyfully bizarre video with director Hype Williams to let people know who they were dealing with. “It helped people understand the type of artist that I am: witty, with a fun, comical sense, but futuristic, too.” Suddenly, everybody wanted a piece of her.

Elliott remembers receiving calls from Whitney Houston, Mariah Carey and Janet Jackson in a single month. “It happened so fast that I’m just now getting a chance to sit back and re-evaluate everything,” she says. “This year has allowed me to look back over my life and be like: ‘Wow.’” When she watches the spectacular video for her 1999 single She’s a Bitch, in which she rises out of the ocean like a bald cyborg, she’s amazed. “I think: ‘Where was my mind at? What space was we in to create records like that?’ So many moments I look back and wish that I knew what I was thinking at the time.” Like a hip-hop Doctor Strange, Elliott was a reality-bender. On hits such as Get Ur Freak On and Work It she made everything elastic – voice, rhythm, language, body – until the usual rules ceased to apply. Both avant-garde and platinum-popular, she revolutionised hip-hop and R&B while also wowing the likes of Thom Yorke, Damon Albarn and Björk. Her videos with Hype Williams and Dave Meyers were no less game-changing than her records, each one a reinvention. She credits Elektra Records for running with her imagination. “Not once did they say: ‘No, you can’t do this.’ I would bring stuff to them and they’d be like: ‘Let’s do it.’ The only time you get pushback is when they realise the budget is a million dollars.” She laughs. “Then they’re like: ‘Wait a minute … ’”

Simultaneously, she and Timbaland created startling hits for other artists, including Tweet, Melanie B and Destiny’s Child, featuring a 16-year-old Beyoncé. “It wasn’t that Beyoncé came in and was loud or ‘Look at me, I’m gonna be the star,’” Elliott remembers. “She was very sweet. But when she went in the booth, that’s when I knew.” Beyoncé later appeared on Elliott’s 2002 track Nothing Out There for Me. “I said: ‘Hey, I want you to rap a little bit.’ And she was like: ‘Miss, if I sound crazy, don’t put this out!’ And I said: “Trust me, B, I’m not gonna allow you to sound crazy.’ She went in there and now she’s rapping better than me!”

In recent years, critics have emphasised the political impact of Elliott’s work. By radiating pleasure and freedom while upending expectations about race, gender and body image, she was an empowering figure, although she insists that was a byproduct rather than an agenda. “Never, ever once did I think of making a political statement. I did what I did. I didn’t know that it would become that for others later.” She enjoys it, though. “To know that it has been taken that way, I’m happy.”

Then, in 2005, Elliott effectively put her solo career on ice. What happened? “Well, I’m going to be honest, there were a lot of things,” she says hesitantly. One was overwork. A stranger to holidays, she was always either working on her own music (six albums in eight years) or someone else’s. “I needed to refresh my mind. Then I got sick, so that was another thing.” In 2008, after three years of chronic fatigue and drastic weight loss, she was diagnosed with Graves’ disease, a thyroid disorder, and treated with radiation therapy. Even once she was able to resume recording, Elliott’s hiatus between albums became self-perpetuating: the longer she stayed away, the harder it was to come back. Without deadlines or financial pressure (she invested wisely), her perfectionism took over. She disappeared into the studio, racking up several albums’ worth of unreleased material. “You end up building up a trillion records,” she says. “It’s easier for me to write for other people and not be as critical. I’m very hard on myself. I’m like: ‘Let me see if I can make something better,’ so you just keep powering on.”

The overwhelming, instant scrutiny of social media exacerbated this self-doubt. Earlier this year, Cardi B tweeted about anxiety and Elliott sympathised: “Many people deal with this … i am one … it’s real.” This wasn’t something that rappers discussed publicly in the 90s. “Anxiety and depression, I’m not gonna lie, I rarely heard that back then,” she says. “But now I hear it a lot. Before social media you really didn’t know what people thought of you but now it’s so in your face that I think it probably gives a lot of artists anxiety. You have a lot of people coming at you, good or bad.” So she stuck to supporting roles on records by the likes of Ariana Grande, Janet Jackson, the Missy-indebted Lizzo and debut recording artist Michelle Obama: Elliott was the highlight of Obama’s 2016 charity single This Is for My Girls. “I wasn’t gonna say no. Y’know, it’s Michelle Obama. Am I really gonna be like: ‘Nah Michelle, I’m busy!’ She made me feel she was in my family. I almost forgot she was the First Lady.”

Now, finally, Elliott is “most definitely” ready to take the plunge and release that album, self-doubt be damned. “This time the label is like: ‘Knock it off, Missy Misdemeanor Elliott!’ Ha ha!”

The good news is that new music means live shows. The bad news is that these might have to take the form of a Las Vegas residency because Elliott’s ideas may be too ambitious to be portable. “It’s going to be a lot because there’s so much going in my mind,” she says. “My mind is like a rollercoaster. It’s like an amusement park. Heh heh heh.” At long last, Missyland is reopening for business.

Missy Elliott’s Iconology EP is out now