The Sarepta Therapeutics (SRPT 0.14%) rollercoaster ride is back on the upswing.

Today, the Cambridge, MA-based company revealed that it's reached an agreement with the FDA on a clinical plan that will give it a shot to win early approval for its Duchenne Muscular Dystrophy drug, eteplirsen, before it completes a larger, Phase 3 trial.

To be clear, this isn't a guarantee: Sarepta still has to produce additional positive data from existing and new studies to prove its case. But it's nonetheless a big deal for Sarepta and children with Duchenne, a crippling genetic disorder with no cure, because it at the very least gives Sarepta the possibility of not having to wait several years before getting eteplirsen on the market. Sarepta CEO Chris Garabedian said on a conference call with analysts this morning, for instance, that if all things go well, the company could submit its application by the end of the year, and win approval in 2015.

"We now have clear direction from the FDA to move our [Duchenne] program forward," Garabedian said on the call.

Investors cheered the news—-shares skyrocketed more than 50 percent in early trading on Monday.

There's a lot here to take in, but here's what the plan is now for Sarepta:

First, Sarepta will run a confirmatory trial of 60 to 80 patients who can walk at least 300 to 450 meters on the standard 6 minute walk test at the start of the study. Those patients will be between 7 and 16 years old, and Sarepta will perform muscle biopsies before and after treatment—the company couldn't specify how often. These biopsies will be used to help establish a correlation between increased dystrophin protein production and patients' increased ability to walk. This study will begin in the third quarter.

Sarepta, however, doesn't necessarily need to finish this study before winning approval of eteplirsen. Based on its discussions with the FDA, the company now has two potential ways to strengthen its case for accelerated approval. One is to add more long-term data from its tiny, 12-patient, Phase 2b study with more follow-up results showing the drug's continued positive effects. Secondly, the FDA will work with Sarepta to get a deeper understanding of the ways the company has been using to measure the levels of patients' dystrophin—the key protein Duchenne patients lack—to help the agency get more comfortable with how Sarepta has been accruing the data, and work through other acceptable ways of quantifying it. Sarepta will also conduct additional biopsies to continue to track patients' dystrophin levels and tie it to their walking ability.

Secondly, Sarepta will also kick off two additional trials to establish eteplirsen is safe in a broader group of patients, and get more biopsy data to show regulators. One of those trials will include at least 20 patients between 4 and 6 years old. The second study will be a like-sized trial that will include older patients (between 7 or 16 years old) who can walk no further than 300 meters on the 6-minute walk test. Sarepta hasn't finalized exactly who can and can't enroll in these studies just yet, but expects to begin the trials later this year, and use data from those studies as part of its NDA filing package.

Lastly, Sarepta is also putting together placebo-controlled trials testing some of its drugs that target Duchenne patients with different genetic variations. Eteplirsen is an RNA-based drug that targets an abnormality in part of the dystrophin gene called exon 51, and helps patients skip past the faulty section of the gene so they can make enough of the protein to keep their muscles working. About 13 percent of Duchenne patients have the form of the disease caused by this particular genetic variation. Sarepta plans to file investigational new drug applications for SRP4045 and SRP4053—which target abnormalities in the exons 45 and 53, respectively—by the third quarter. Sarepta wants to have those trials well under way by the time the FDA begins reviewing its application for eteplirsen.

Sarepta's broad plan is to establish a franchise in Duchenne first by winning approval of eteplirsen. It then wants to move drugs forward behind eteplirsen that target a different genetic variation triggering Duchenne, hopefully getting them approved on their ability to increase dystrophin production alone. Sarepta has 7 other drugs behind eteplirsen that, combined, could cover about half of the Duchenne population.

The FDA, however, has been very wary of establishing dystrophin production as a valid study goal in support of accelerated approval. This is why, for instance, the agency is working with Sarepta and the pathologists in the company's trial to get a deeper look at the dystrophin data, and why it wants biopsy results.

It's been an up-and-down ride for Sarepta to get here. Sarepta made the bold move of filing an NDA with the FDA in July based on its small, Phase 2b study of eteplirsen, and shares soared. A few months later, however, the FDA called that filing "premature," putting Sarepta in the daunting hole of having to run a long, expensive study, and meaning patients might have to wait several years before getting access to the drug. Shares plunged more than 50 percent as Sarepta's future became largely unclear.

The big question since has been whether the FDA would reconsider, or give Sarepta an opening for a quicker path. While there's a lot still left to prove, Sarepta now has that chance.

This article originally appeared on Xconomy, along with: