There’s a line of thinking that holds that everything in the music business is cyclical, with periods of crass commercialism fostering healthy underground music scenes that eventually make enough noise to catch the ear of the mainstream music industry, which then markets this new brand of rebel rock to a public hungry for something new, exciting, and different. The subsequent creative explosion prompts underground bands to clamor for major-label contracts, until it’s almost impossible to distinguish the "genuine" from the "manufactured" and the whole process starts all over again. The alternative-rock explosion of the ’90s was a textbook example of this process in action, but it’s been occurring ever since Elvis shocked the world with his pelvic gyrations, and it’s led to at least one major pop-music revolution every decade leading up to the ’90s.

Whereas large-scale trends are often hard to detect until well after they’ve established themselves, the local variety are usually much easier to spot, especially in a city with a music scene as vital as Boston’s. Just think back to the early ’90s, when dozens of new artists were making challenging and exciting music in clubs all over town. It didn’t take long, once Nirvana turned the industry on its head, for major-label scouts to descend on the Hub; within a year or two performers like Tracy Bonham were getting signed practically right out of the rehearsal space, with just a couple of gigs under their belts and a handful of songs ready to record. Once it saw that kind of big-label money being thrown around, your average garage outfit began to tailor its sound to fit the style of the moment, whether that was grunge, alternative, or neo-punk. Unfortunately, there’s room for only a couple of Green Days and Offsprings on the charts and on radio, so most of those bands went nowhere. And for a time, the local music scene seemed as tired and played out as flannel fashions and goatees, with major-label talent scouts becoming more interested in molding the next Backstreet Boys or Britney Spears than in fishing around in smoky clubs for yet another pop-punk trio who might just get picked up by the next Warped Tour.

But such a scene is also the perfect environment for good things to start happening again on a local level, as independent labels once again reassert themselves and creativity flowers in the absence of high-pressure commercial expectations. And it’s turned out to be the ideal setting for Mark Kates — a Beantown native who got his start doing publicity for Mission of Burma in the early ’80s before moving on to big LA gigs as a Geffen A&R honcho and then as president of the Beastie Boys’ recently defunct Grand Royal label — to return not only to Boston but to the realm of the independent music label.

Kates, who showed up around town last summer to check on things in his old home town and to help A&R a live album by the massively popular jam band Dispatch, is now re-entrenched in Boston, and he hasn’t wasted any time establishing himself as a vital behind-the-scenes presence. He was involved in the hugely successful recent Mission of Burma reunion shows, and that brought him full circle because, as he explains, "Mission of Burma were the reason I got involved in the music business to begin with." We’re sitting outside his small office in the Porter Square, where he and one assistant have set up shop for his newly christened Fenway Recordings record label. It may be a big step down from the offices he inhabited at Geffen and Grand Royal, but he’s not complaining.

"I’ve been trying to get back here practically since I left. Boston-versus-LA is not even a question for me. LA was very good for me, but I think it’s culturally pretty dead out there, and the business there is in complete turmoil. Artists are raising money to battle the labels and, well . . . it’s just a mess. Plus, I don’t think there’s ever been a time here in Boston where there were so many different things that were really good in so many different genres having nothing to do with the conventional business. I don’t think people are walking around here bummed out that they’re not signed."

Kates’s excitement about the current state of the Boston music scene is infectious, and he communicates the sense that through sheer force of will and determination he’s going to find a way to make Fenway Recordings work. He’s already signed two promising artists whose debuts are scheduled for release in the next few months: former Bosstones guitarist Nate Albert’s punkishly poppy outfit the Kickovers, whose line-up also features former Weezer bassist Mikey Welsh; and Consonant, Mission of Burma bassist Clint Conley’s new band, and his first major musical project since Burma’s break-up. Consonant’s homonymous debut has more than a hint of Burma’s poppier side in it — not too surprising when you consider that Conley was responsible for penning the band’s poppier numbers ("Revolver" and "Academy Fight Song" being two of them).

But Fenway Recordings is not committed solely to signing Boston-based artists. The label’s first release, and one of the inspirations for Kates’s decision to start the company, is a 12-track compilation titled In Our Lifetime Vol. 1. It does feature a couple of Boston bands (there’s a Cracktorch cut and a Kickovers tune attributed to the Brakes, which was the first name Albert picked for his band). But In Our Lifetime is all over the map, with tracks by the Irish band Ash, Texas wunderkind Ben Kweller (formerly of Radish), and Ocio, a Buenos Aires–based electronic outfit whose chill-out "Quasar" ends a disc that opens with a foursome of hard-hitting guitar-driven numbers.

"Despite the fact that my first two artists signed are from here," Mark goes on, "and despite the fact that I’ve found it so ripe here and as each day goes by I feel stronger and stronger about the situation here right now, I want to build a series of compilations with a brand name that people look for. And I want to be able to put out anything that I find and like. I mean, I’m going to England with Mission of Burma, and I know I’m going to come back with a suitcase full of good stuff. So I’m trying to cast my net wider. But I keep getting great stuff from here in Boston, so I think my third compilation is going to be all Boston-based bands. The thing that’s driving me is that there’s a ton of great music here. How much of it is going to succeed? I don’t know. But I like my odds based on my track record in the business." And about that track record: the CDs Kates has been associated with on the A&R end include Nevermind, Odelay, and Live Through This.

JUST ACROSS THE RIVER from Kates’s office stands a Boston institution that has a pretty decent track record of its own in a very different sphere of the business. Berklee College of Music has dozens of jazz heavyweights among its faculty and alumni (most famously, Pat Metheny), and it continues to be one of the top schools in the world for the study of jazz. But one of the worst-kept secrets in town is that Berklee isn’t just a home for jazzbos. Along with producing a number of commercially successful mainstream rock/pop artists — Melissa Etheridge and Paula Cole, to name two — the school has counted among its students a number of better-known alternative-rockers who went on to emerge from the local scene, including Juliana Hatfield, Aimee Mann, and Tracy Bonham. By its very nature as a music school, Berklee has always acted as a magnet, attracting to town a continuous stream of aspiring musicians who then mix and mingle with the indigenous rock scene — even if that’s not something that your average area punkabilly garage band would want to admit.

And now it’s going to be harder than ever to maintain the illusion that there’s some wall of integrity separating the schooled technicians at Berklee from the passionate, self-taught, DIY artists from the underground scene, thanks to Shekinah: 13 Artists, a compilation of 13 tracks by 13 women artists from Berklee that was put together by the school’s in-house Heavy Rotation label but is being manufactured, distributed, and marketed by the major label Epic. The disc — whose artists performed at the school back on February 6 — showcases a side of Berklee that’s too often overshadowed by its well-deserved reputation as a jazz stronghold, and much of what you’ll find on it isn’t so different from the music that’s being played by unmatriculated musicians in the grittiest local clubs every night of the week. There is a pronounced leaning toward the kind of confessional folkish pop you’d expect from a compilation of female singer-songwriters who came together in the wake of a couple years of Lilith Fairs. And there’s one track, Rhea’s "With or Without You," that’s aiming for Destiny Child’s brand of hip-hop-inflected R&B. But there are also two dark and grungy metal tracks — Mancain’s "Please the Devil" and Amanda Williams’s "Low" — as well as the sultry, techno-textured dream pop of Polina’s "Out of My Mind."

"I think some people who have been to school here don’t want to be known as having gone to Berklee because there’s a negative stereotype," admits Kristin Cifelli, who contributes the mellow and moody "Martyr" to Shekinah, and who graduated from Berklee only to stay on as a voice teacher. "But we’re not all jazz musicians and we’re not all geeks. I also think that out of state it’s cooler to have gone to Berklee."

"Old stereotypes don’t die easily," admits Gary Burton, one of the deans in charge of curriculum at Berklee. "We started in the ’40s, when jazz was the commercial music of the time. The college really started adding pop music to the curriculum around the early ’70s. By the mid ’80s, I would estimate that the balance between students interested in pop and students interested in jazz was about 50-50. And if you look at our curriculum, we made a big move about 10 years ago to go through all the course materials and even out the jazz and the pop."

Shekinah came not from a class dedicated to pop music but from a class taught by Jeff Dorenfeld that focuses on the business of putting out records. "My background is rock music, so that’s the direction I took the class in," Dorenfeld admits. "And part of the reason I put this record together is to represent a particular side of Berklee." But it was only after he and his students realized the range and depth of the talent they’d compiled that the deal with Epic began to make sense. So what started out as a class project has turned into a disc that may just help build a bridge between the rock scenes at Berklee and Boston.