NEW YORK (The Deal) -- Jana Partners' $2 billion investment in Qualcomm (QCOM - Get Report) and its attendant activist campaign has been constructive. Until now. The relationship turned bumpy in late June after the technology company's executive chairman said that there were no plans to spin off a chipmaking and tech licensing business.

Those comments came after Jana Partners in April began publicly urging Qualcomm to consider whether a "partial or full" separation of those business units made sense. Founder Barry Rosenstein contends that there clearly is a "sum of the parts" discount in the stock, and he had been engaging the company for several months before launching the public campaign.

Rosenstein made a variety of demands--at least two of which appear to have been partly met so far: Qualcomm authorized a $15 billion share repurchase program, though that also came after the resolution of a major antitrust dispute in China. The company also hired outside consultants to do a cost review.

Rosenstein argues that his firm's thesis is not "predicated" on a partial or full separation of the licensing and chipset business, but Jana Partners probably wasn't too pleased with the decision to keep the units intact. A Jana spokesman declined to comment. But pressing companies to spin off divisions is a key part of Jana's modus operandi for unlocking shareholder value. It took only 12 days for Rosenstein's campaign at ConAgra Foods CAG to drive that company to spin off its private brands business. And tech outsourcer Computer Sciences Corp. (CSC) in May announced it would split into two businesses only a few months after Jana Partners launched a campaign seeking a strategic review.

If Qualcomm fails to cut costs, replace "overtenured" directors, or deploy its buybacks faster in the coming months -- all things Jana wants -- the activist fund's stance could turn increasingly hostile. Expect to hear more about at least some of Qualcomm's responses at the company's July 22 earnings call. CEO Steven Mollenkopf said in April that the company will report on the cost assessment on that call.

It's not clear, though, exactly what Jana could do if Mollenkopf digs in his heels. With no special shareholder meetings and no ability to act by written consent, Jana will have to wait until next year to launch a proxy contest. Director nominees are due by Dec. 10.

A contest running to its conclusion at the $101 billion market-cap company would be monumental and in many ways unprecedented. It would be the biggest contest ever, hugely expensive -- surpassing the two battles that currently top the list. Both of those -- Trian's battle at DuPont (DD - Get Report) -- and Pershing Square's 2009 contest at Target (TGT - Get Report) --were embarrassing failures for the activists.

Jana's most recent contest, in 2013, involved another bid company -- Agrium (AGU). Rosenstein's nominees lost after an acrimonious 10-month campaign. The disappointment there -- and the magnitude of a Qualcomm contest -- is likely weighing on Rosenstein. And Qualcomm likely senses some vulnerability.

The company, though, also has some weaknesses. In March, roughly 42% of shareholders opposed Qualcomm's executive pay packages, suggesting that there is a large disgruntled group of investors who believe the compensation plans aren't aligned with returns. Qualcomm argues that a key part of the package involved one-time retention grants to Mollenkopf, as he was being recruited to fill Microsoft (MSFT - Get Report) CEO post. Next year's executive pay will not be as rich, according to a spokesman.

Nevertheless, speaking on the sidelines of a recent conference, Rosenstein suggested that a large negative executive pay vote often hints at other issues afflicting a targeted company. "It's not dispositive but it could be indicative of a deeper problem," he said.

Qualcomm also has maintained a "worst in class" governance rating from Institutional Shareholder Services, a 10 out of 10 ranking that hasn't improved in recent months despite Jana's advances. The ISS report, obtained by The Deal, raises a number of red flags that gibe with Jana Partners' concerns, including worries about over-tenured directors and a "pay for performance misalignment."

And while no activist has won a proxy contest at a $50 billion-plus target company, a few large director-election battles have settled, including a campaign led by an ex-Obama administration task force member at General Motors (GM - Get Report) that concluded this year, and Carl Icahn's contest at eBay (EBAY - Get Report) last year. So Qualcomm and Jana could work out a deal to avoid a costly proxy battle.

Such a deal might include making some strategic acquisitions, and some shareholder-friendly changes to executive pay packages.

The chipset business spinoff, though, could be a major sticking point. Jana points to an analyst report from research firm Arete suggesting that the spinoff and public listing of the chip business would "make for an attractive take-out" by Intel (INTC - Get Report), which "has long struggled to keep up with the radio features of Qualcomm's modems and is losing over $3 billion a year in its mobile division."

December may seem a long way off, but for Qualcomm, the weeks and months will pass quickly.