In 2002 the pastor, Father William Gulas, OFM, was killed by Brother Daniel Montgomery, OFM, and to hide the crime Montgomery set the parish friary and offices on fire. Montgomery later admitted to the crime and was sentenced to life in jail in 2005. Father William was succeeded by Father Michael Surufka OFM. Surufka formed the Franciscan Development Corporation to help develop new residences in the neighborhood.
In 2004, St. Stanislaus completed a $1.4 million dollar renovation of the church's interior and on 8 May of that year, it was re-dedicated as the Shrine Church of St. Stanislaus.
In 2008, the administration of the parish was transferred from the care of Sacred Heart Province of the Order to Assumption Province, which is the Polish-American province of the Order.
In April 2007, a group of parishioners traveled to Kraków and brought back an icon, written in tempera by Polish iconographer Mado Anna Kucharska, depicting St. Stanislaus with John Paul II. Kucharska, after a transatlantic flight that week, added a golden Halo around John Paul's head on April 29, 2011. "We will have the first official image of Blessed John Paul II in the world," claimed Surufka. "I don't know anyone else who has an image of John Paul and is ready to unveil a halo seconds after he is beatified." The Beatification of Pope John Paul II was held on May 1, 2011.
In 2011, after 105 years of service, the Franciscan order left the Shrine Church of St. Stanislaus. "Our numbers are diminishing and we're aging," said Surufka. "The bottom line is we just don't have the men."
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