JetBlue Airways (NASDAQ: JBLU) reported disappointing results on the same day the antitrust trial debating JetBlue’s planned acquisition of Spirit Airlines kicked off. The combined headwinds are weighing heavily on the stock, sending shares of JetBlue down as much as 17% on Tuesday.

JetBlue faced “staggering” challenges in the quarter

It has been a difficult earnings season for airlines, with most reporting strong summer holiday traffic but weakening trends heading into the fall. Unfortunately, JetBlue didn’t enjoy as robust of a summer season due to air traffic constraints at key airports.

JetBlue lost $0.39 per share in the quarter, worse than the $0.25-per-share loss analysts had expected. The company also warned it expects to lose between $0.35 and $0.055 per share in the fourth quarter and between $0.45 and $0.65 per share for the year, which is below the $0.15-per-share and $0.24-per-share loss estimates.

“While we have been able to offset some of the costs associated with the challenging operational backdrop, the sheer magnitude of the air traffic control and weather-related delays has been staggering,” CFO Ursula Hurley said in a statement. “We remain focused on controlling what we can control, including our structural cost program and fleet modernization plans.”

Consolidation could be part of the path to profitability. Last year, JetBlue won a bidding war for control of Spirit Airlines, but that deal has been challenged by the U.S. Department of Justice. The antitrust trial to decide whether the merger can proceed began on Tuesday.

Is JetBlue a buy after its earnings disappointment?

The macro challenges that caused JetBlue to miss expectations are hardly unique to one airline, but they do seem to be hitting JetBlue harder than most. The airline’s route network is focused on the northeast U.S., where congestion is a continuous issue. JetBlue also doesn’t have the resources to match larger airlines when it comes to pilot compensation, making it harder to hire qualified personnel.

The Spirit deal adds considerable additional uncertainty. JetBlue would benefit from the influx of pilots and newer, fuel-efficient aircraft that Spirit would bring, but having to integrate another airline in a time of falling demand would be a challenge. If the airlines lose in court, JetBlue could be responsible for a $400 million breakup fee payable to Spirit.

Add it all up and there is a lot of reason to believe that things won’t turn around quickly for JetBlue, and a lot of ways conditions could get worse before they get better. It’s no wonder investors are running for the exits on Tuesday.

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Lou Whiteman has no position in any of the stocks mentioned. The Motley Fool has no position in any of the stocks mentioned. The Motley Fool has a disclosure policy.