Seagate Technology reported today that it had a net loss of $496 million, or $1.02 a share, for the second fiscal quarter ending January 2.

Revenue for the quarter was $2.3 billion, which matched the low end of revised expectations for the quarter from Seagate itself. But analysts had expected a loss of just 5 cents a share and revenues of $2.46 billion. A year ago, Seagate’s revenues were $3.42 billion.

Seagate’s loss includes $18 million of one-time charges associated with acquisitions, $94 miillion related to restructuring and accelerated depreciation, and $271 million in charges related to an adjustment in the company’s valuation allowance for deferred tax assets.

Seagate’s longtime chief executive Bill Watkins and his chief operating officer Dave Wickersham resigned last week. The Scotts Valley, Calif.-based storage company also said it was laying off 6 percent, or 2,950 employees, of its worldwide staff. It has also cut staff and executive salaries.

Stephen Luczo, the new CEO (and existing chairman), said in a conference call that the company is planning for a pricing scenario that is similar to the past few quarters. He said that pricing in the past few quarters has been the worst in the industry’s history.

After hours, Seagate’s stock fell 22 cents to $4.03 a share. Before the earnings, Seagate’s shares rose 37 cents to $4.25 a share. Luczo said the good news is that the team in place at Seagate is the same one that helped turn around the company in years past. Luczo said there is so much uncertainty from the economy that the company is having a much harder time predicting its own future.

Both Seagate and rival Western Digital have said they are cutting back on their production capacity. Seagate is trying to be flexible enough to bring capacity back on line if demand revives. Luczo said he believes everyone in the industry is doing the same thing. Luczo said he is committed to getting back to profitability in the long run.