On Rev. Sheelagh A. Clarke’s first day as Rector of St. Stephen’s Church in Millburn, she had a tough time even getting to it.

Just two days prior, Hurricane Irene had flooded parts of town, as well as other towns between her house in Scotch Plains and the church, and she kept running into closed roads.

When she finally got to the church, there were trucks out front and crews trying to pump the water and waste out of the basement, where the preschool had been.

She rolled up her sleeves and got to work, getting to know her parishioners quickly as they worked side by side, removing contaminated rubber chips from the playground and throwing out every toy and piece of furniture in the preschool.

“None of it could be salvaged because it was contaminated with the most disgusting, smelly water and muck,” she said. “It was heartbreaking. There was about $72,000 worth of equipment that looked fine but dirty and could never be used again.”

The church got temporary permits to house the 40 students displaced from the basement upstairs in the church while Clarke brought in contractors and subcontractors and restored the preschool.

Five weeks to the day of Irene’s destruction, bright, clean and airy classrooms welcome children back.

“We rebuilt everything from the ground up – really, from beneath the ground  up,” Clarke said.

Other parts of the church were also destroyed and the floorboards and many of walls that were not destroyed had to be drilled into to air them out and dry them out.

The historic old Rectory, where the interior had been lovingly restored, was also destroyed as flood waters forced their way into the radiator system and was sprayed out throughout the house, destroying floors and causing ceilings to give way.

“It’s tragic, really,” she said.

The church is slowly back. On the wall near the sanctuary, which luckily did not suffer damage, is a storyboard telling the tale of the flood, the aftermath and the rebuilding up til now.

The damage estimates are at $275,000 but the rector thinks when all is said and done it will be closer to $3,000. Luckily, churches tend to have good insurance and insurance is paying the bulk of the tab – except for a $55,000 deductible, which the church is trying to pay for through fundraisers instead of loans.

“You don’t get trained for this,” she said. “I have felt like a general contractor since I got here.”

The children of the church held a carwash and raised $810, the cemetery history tour raised about $1,500, and so far, donations have amounted to $28,000.

The church sits on Main Street sandwiched between Church and Rector streets, which was one of the areas of town hardest hit by the floods that occurred after Irene dumped nine inches of rain after the ground had been heavily saturated by heavy rain in the week leading up to the storm. The days preceding the storm brought several inches of rain.

Residents of the Washington neighborhood near Taylor Park say the Rahway spilled out of its banks and backed up at the pond’s floodgates, pushing several feet into their basements.

And the church was one of the first hit as water rushed through, filling the pre-school with four to five feet of water.

On the morning after the rains of Irene pummeled the area, Clarke’s assistant Betty Innemee was the first to arrive at the church and the first to see the condition of the Rectory.

“I heard water rushing into the living room,” she said. “I went in there and part of the ceiling came down right in front of me. After that, I really had to sit on the front steps for bit and gather myself. We had just finished the restoration.”

“That’s the painful piece of it,” Clarke said. “The loss of all that work and love that went into keeping the historical aspect to this place. It’s all gone.”

This coming weekend, Splurge Bakery is hosting a wine and dessert fundraiser for the church.

“We’re halfway there, and it seemed like a good time to celebrate what we’ve done so far,” Clarke said. "This [rebuilding] has really galvanized everyone. And as they say, 'It's an ill wind that blows no good.' "