Houston Texans (2006–2013)
Kubiak was named the second head coach in Houston Texans history on January 26, 2006, replacing the fired Dom Capers. In his first season with the team, Houston finished fourth in the AFC South with a 6–10 record. The Texans ended the 2007 season at 8–8, a non-losing record for the first time in team history. The Texans had their second non-losing season, again finishing 8–8, in the 2008 season.
The following season under Kubiak, the Texans achieved their first winning season in franchise history when they overcame a 14-point fourth-quarter deficit to defeat the New England Patriots 34–27 at Reliant Stadium, finishing the 2009 season 9–7. They missed the playoffs on a tiebreaker with the New York Jets. On February 2, 2010, with a year left on the original deal he signed, the Texans signed Kubiak to a three-year contract extension through 2012.
In the 2010 season, Houston started off strong with a record of 4–2 heading into their bye week (Week 7). However, Kubiak's promising campaign quickly turned disastrous as the Texans lost eight of their final 10 games, placing them third in the AFC South, with a record of 6–10. The Texans ended up fourth in passing yards, seventh in rushing yards, and third in overall yards. But the 2010 Texans defense was arguably one of the worst in the league, finishing last in passing yards allowed and tied for last in passing touchdowns allowed.
The Texans responded to the 2010 poor defensive showing by firing defensive coordinator Frank Bush, secondary coach David Gibbs, linebackers coach Johnny Holland, and assistant linebackers coach Robert Saleh. Kubiak, a ball boy for beloved former Houston Oilers head coach O.A. "Bum" Phillips in the 1970s, hired long-time friend, and Bum's son, Wade Phillips to take over as the Texans' new defensive coordinator on January 5, 2011. Phillips became available after being fired as head coach of the Dallas Cowboys halfway through the 2010 season. Phillips was allowed to bring in his own assistant coaches. The Texans signed two high-profile free agent defensive backs, Johnathan Joseph and Danieal Manning, and used their first five draft picks, including two in the second round of the 2011 NFL draft, on more defensive players.
The 2011 NFL lockout limited the time coaches had with players in the preseason, but Phillips turned the defense he took over from 30th overall in 2010 to second overall in 2011. Despite debilitating injuries to elite players including wide receiver Andre Johnson and NFL top running back Arian Foster, as well as the devastating November 13, 2011, loss of quarterback Matt Schaub, who was having a solid year, for the season, the Texans secured their first AFC South Championship and first appearance in the NFL playoffs. The Texans, with rookie fifth-round selection T. J. Yates at quarterback, defeated the Cincinnati Bengals by a score of 31–10 on January 7, 2012, in the first playoff game in franchise history, with a record crowd of 71,725 at Reliant Stadium.
Kubiak was named the AFC Coach of the Year by NFL 101 after leading the Texans to a 10–6 regular season record and the franchise's first division crown, playoff berth and playoff win in 2011. Texans owner Bob McNair rewarded Kubiak with a new three-year contract on June 14, 2012. Kubiak turned down a four-year deal for one that expired after the 2014 season.
The 2012 season saw the Texans start 5–0 for the first time in the franchise's history. The Texans finished the season a franchise-best 12–4 and defeated the Cincinnati Bengals in the Wild Card Round for the second straight year before falling to the New England Patriots by a score of 41–28 in the Divisional Round.
On November 3, 2013, Kubiak collapsed as he was walking off the field at halftime of the game against the Indianapolis Colts. He was put on a backboard and stretcher and transported to the hospital as a precautionary measure. Initial reports stated that he had not had a heart attack. An NFL report on Monday, November 4, 2013, indicated that he had suffered a transient ischemic attack (TIA), or relatively brief, non-permanent symptoms of disorientation, confusion, dizziness, forgetfulness, and/or vertigo (among many other possibilities), that occurs when a blood vessel or vessels in part(s) of the brain are temporarily but not permanently blocked, usually by a stationary clot (a thrombus) or one that has broken off and traveled to occlude another area (an embolus). Especially if they are not properly treated in a timely manner the way Kubiak's was, they can mean that a more permanent stroke (or cerebrovascular accident, CVA) can and likely will eventually happen. In Kubiak's absence for the second half between the Colts, defensive coordinator Wade Phillips assumed the head-coaching duties and was the acting head coach for the remainder of the game.
On December 6, Kubiak was fired from the Houston Texans with three games remaining in the 2013 season. He finished the 2013 season with a 2–11 record and was replaced by defensive coordinator/interim head coach Wade Phillips. Kubiak had a 61–64 regular season record and a 2–2 playoff record as the Texans' head coach.