Some controversy resulted after the media highlighted a number of rollovers involving Explorers and Mountaineers fitted with Firestone tires.

For 1996, the Acura SLX (Isuzu Trooper), Infiniti QX4 (Nissan Pathfinder), and the larger Lexus LX450 (Toyota Land Cruiser) were introduced together.

As part of a 1998 model revision, the Mountaineer was given a model-specific grille and headlights, larger wheels, and a new rear hatch design.

The first-generation Mercury Mountaineer was introduced in a single trim level, offering many optional features of the Ford Explorer Eddie Bauer and Limited as standard.

[5] Ending its chassis commonality with the Ford Ranger pickup truck, the Explorer/Mountaineer adopted a dedicated platform, introducing all new underpinnings and a four-wheel independent suspension to the model lines.

Though sharing much of the same body (from the firewall rearward), designers began to give the model line an identity distinct from the Explorer.

The traditional Mercury silver waterfall grille was made rectangular (along with headlamps wrapping into the hood), introducing silver-trimmed taillamps and satin-silver wheels and badging.

In various forms, style elements of the 2002 Mountaineer would appear across the Mercury line during the 2000s, including the Grand Marquis, Montego, Milan, Monterey, and Mariner.

Upper trim versions offered features including a rear TV/DVD player, rear ceiling air vents, chrome exhaust tip and roof rack, and body-color bumpers.The third-generation Mercury Mountaineer was introduced for the 2006 model year, again serving as a counterpart of the Ford Explorer.

In contrast to the Explorer, the third-generation Mountaineer retained many styling elements from the previous generation, introducing clear-lens taillamps, fender-mounted turn signal repeaters, larger wheels, satin-silver trim for the sideview mirrors and bumpers; the grille and tailgate received larger Mercury emblems.

As an option, the Mountaineer Premier offered power-retracting running boards (a feature adopted from the larger Lincoln Navigator, not introduced on the Explorer until 2007).

The navigation system was upgraded, including traffic flow monitoring and live updates on fuel prices from nearby service stations.

For 2000, the Mountaineer was the third-best-selling Mercury (behind the Sable and Grand Marquis); ten years later, the model line had become the slowest-selling vehicle of the brand.

Following the June 2010 announcement by Ford Motor Company to shelve the Mercury brand, 2010 would be the end of Mountaineer production; the final vehicle was produced on October 1, 2010.