Moving to clean house amid an organizational crisis, the National Rifle Association cut ties with its second-in-command, Christopher W. Cox; severed its relationship with Ackerman McQueen, its estranged advertising firm; and shut down live production at its online media arm, NRATV.

The steps took place within a brief span on Tuesday night and Wednesday morning.

The resignation of Mr. Cox, the gun group’s top lobbyist and the architect of its legislative strategy, was communicated to the N.R.A.’s board and employees on Wednesday. The news comes days after a court filing by the N.R.A. implicated him in a failed plot to oust Wayne LaPierre, the organization’s chief executive, an allegation Mr. Cox has disputed. Last week, The New York Times reported that the N.R.A. had suspended Mr. Cox.

Mr. LaPierre, in a message sent Wednesday to employees and board members, said he had accepted Mr. Cox’s resignation and wanted “to thank Chris for his service to the N.R.A. and for his efforts to advocate for the Second Amendment.” He noted that Mr. Cox had been “placed on administrative leave” pending an investigation into the claims against him, and said, “Naturally, that pursuit will continue in the interest of the N.R.A. and our members.”

The development is the latest in an already tumultuous year for the N.R.A. The gun group has struggled to right its finances; faced investigations in Congress and by the New York attorney general; and witnessed a leadership struggle that pitted Oliver North, until recently the N.R.A.’s president, against Mr. LaPierre.