Tropical Storm Allison caught the city by surprise, dropping more than three feet of rain in some areas and causing deadly flooding and billions of dollars in damage.
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In Texas, 23 people died as a result of the storm, which formed on June 4, 2001, and then first made landfall the day after.
The storm made its way up the state after the initial landfall, before moving back over Houston four days later, dumping historic amounts of rainfall.
Parishioners of the Soldiers of the Cross Church are incredibly thankful now, but when the rain started the evening of June 8, 2001, it was so much water, so fast.
"That night, Allison, ooohhh, all of our families had to rescue the elderly from water...carrying our kids," said Pastor Joel Mondejar with Soldiers of the Cross Church.
PHOTOS: Remembering Tropical Storm Allison
By the time they got to the safety of an overpass two blocks away, there was nothing left of the church compound they'd built.
"It was like a big lake and just half of the house you can see," Mondejar said.
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The church owned a block of land just off the Eastex Freeway for the house of worship and nearly a dozen church members' homes. Theirs were some of the more than 70,000 Houston-area homes damaged or destroyed by Allison.
Eventually, the Harris County Flood Control District decided to buy out the entire neighborhood -- 245 properties -- for a flood control project and the compound was bulldozed. They didn't know where they would end up.
Back then, rain-swollen bayous had taken over and downtown was flooded.
The Alley Theater was ruined and freeways became parking lots of abandoned and useless cars and trucks. Thirty-thousand people needed emergency shelter after Allison. There was $5 billion in damage.
"I think it equates to 32 trillion gallons of water, which I understand is enough to meet the United States' water supply for a year," said Heather Saucier, with the Harris County Flood Control District.
Since then, the Harris County Flood Control District spent at least $1.5 billion widening bayous and getting the region ready for the next big storm.
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Tens of thousands of Houstonians had to rebuild.
Pastor Mondejar's church bought 40 acres of land on a hill in Kingwood and made it even taller. All the flooded families are now back together in new homes within walking distance of their church, in a place they view as the answer to that prayerful question asked on a flooded overpass 16 years ago.
"The answer was a lot better place," Mondejar said.
So many people had to move to a better place after Allison came through. There was 20 inches of rain in spots from the Houston Ship Channel all the way to FM 1960.
At Mondejar's old church, 36 inches of rain fell. Now, there are 1.1 million new Houstonians since the tropical storm rolled through. A lot of them still need to prepare.
Approximately $1.5 billion of the $5 billion in damage caused by Allison came from the Medical Center.