On 24 May 1998 Villarreal sealed promotion to the Primera División for the 1998–99 season, which started with an intimidating match against giants Real Madrid in the Santiago Bernabéu. After a difficult season, Villarreal were again relegated to the Segunda División for the 1999–2000 season, in which they finished third, again earning promotion to La Liga de las Estrellas, the Primera División, where they have remained up to the present day.
FC Villarreal After finishing seventh a year later, Villarreal stayed near the bottom of the table for two seasons before defeating the Dutch team Heerenveen in the final to win their first European title, the Intertoto Cup in the summer of 2003, thereby qualifying for the UEFA Cup tournament.
FC Villarreal The 2005–06 season brought the club considerable European success and recognition, due to their consistent performances in the Champions League. In the qualifying
El Submarino Amarillo drew Italian giants Internazionale in the quarter-finals of the Champions League. The first leg was played at the San Siro on 29 March 2006. Playing at the San Siro, Diego Forlán scored inside the first minute of the match, but Villarreal lost 2–1 as Inter took a lead to the return leg at El Madrigal on 4 April. Villarreal, however, continued their unbeaten home record in the Champions League
as they beat the Italian giants 1–0 in the second leg to qualify for the semi-finals on the away goals rule (the tie ended 2–2 on aggregate, but because of Forlán's goal in Milan, Villarreal advanced). During that game, left-back Rodolfo Arruabarrena turned a back header from Juan Román Riquelme free kick past Inter's goalkeeper Francesco Toldo to score the decisive goal of the tie. In the semi-finals, Villarreal narrowly lost out to Arsenal on a 1–0 aggregate scoreline following Arsenal's goalkeeper Jens Lehmann's save of Juan Román Riquelme's last-minute penalty. Villarreal signed Robert Pirès from Arsenal in the summer following their Champions League semi-final defeat. Pires starred for the club until his departure at the end of the 2009-2010 season. The 2006–07 season started very badly but Villarreal were able to qualify for the UEFA Cup after eight consecutive wins. "The Yellow Submarines" were 13th after Round 30 of La Liga, but they climbed to finish fifth at the end of the season.The club automatically qualified for the 2008-09 UEFA Champions League, due to them finishing second in La Liga the previous season. They drew Manchester United, for the second consecutive campaign, Celtic, and Aalborg
BK. They made a good start by holding current European champions Manchester United to a goal-less draw at Old Trafford, a third 0–0 draw in a row against the English giants. A first win was sealed on 30 September by beating Gordon Strachan's Celtic 1–0 at El Madrigal, courtesy of a Marcos Senna free-kick. On 21 October, during a Champions League match against Aalborg, they scored six goals to three. The Spaniards went ahead through the knock-out stage after drawing 2–2 with Aalborg in Denmark and drawing goalless once again against the Lancastrians, on the last group-stage match, they lost to a already eliminated Celtic.In the knock-out stage, they faced Panathinaikos, which left Villarreal with a 1–1 away advantage, despite this the Greeks were to lose 1–2 in Athens. Villarreal reached the quarter-finals for the second time in two tries, and were once again paired with Arsenal. The first leg saw a 1–1 draw by a free-kick by Marcos Senna, neutralized by an Emmanuel Adebayor volley. Theo Walcott, Emmanuel Adebayor, and Robin van Persie secured a 3–0 win for Arsenal on the return, knocking Villarreal out of the tournament.
For the 2009–10 season, Villarreal saw UEFA Europa League position, going ahead NAC Breda with ease by a 2–9 aggregeate victory. The share Group G with Levski Sofia, who they defeated 1–0 on their debut, and with Lazio and Red Bull Salzburg. They came 2nd in that group, behind Red Bull Salzburg. Consequently, Villarreal was drawn against VfL Wolfsburg -- who had dropped out of the UEFA Champions League -- in the Round of 32. Playing at home first, Villarreal secured a 2-2 draw. In the return leg at Wolfsburg's Volkswagen Arena, however, Villarreal would succumb to defeat by a 4-1 scoreline. This ended their European ambitions for the 2009-10 season.


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