According to a Wednesday morning Senate whip notice, S. 990 will also be the legislative vehicle for the Patriot Act extension. A Tuesday filibuster from Sen. Rand PaulRandal (Rand) Howard PaulSenate approves .3 trillion spending bill, sending to Trump GOP senator threatened to hold up bill over provision to honor late political rival: report Conservatives balk over funding bill ahead of shutdown  MORE (R-Ky.) prevented the Senate from taking up the Patriot Act extension by itself.

Instead, the Senate will take up several amendments to S. 990 from Senate Majority Leader Harry ReidHarry Mason ReidGOP pushes to change Senate rules for Trump Trump presses GOP to change Senate rules Only thing Defense’s UFO probe proves is power of political favors MORE (D-Nev.) on Wednesday. The key amendment would add to S. 990 the Patriot Act extension language, allowing U.S. intelligence officials to conduct roving wiretaps, access business records, and conduct "lone wolf" surveillance until June 1, 2015.

Reid on Tuesday filed for cloture on the bill, which should allow the Senate to vote on the package on Thursday. Reid's effort was aimed at avoiding Paul's filibuster and amendments to the Patriot Act bill that he wanted to pursue.

Assuming the Senate can pass the bill Thursday, the House would have to quickly act on the same bill in order to avoid having the Patriot Act authorities expire on Friday.

But one possible hurdle to these plans is whether every senator can support the House version, which would only extend the small-business programs for four months. According to a Senate staffer, Senate Small Business Committee Chairwoman Mary LandrieuMary Loretta LandrieuSenate GOP rejects Trump’s call to go big on gun legislation Project Veritas at risk of losing fundraising license in New York, AG warns You want to recall John McCain? Good luck, it will be impossible MORE (D-La.) is pushing for at least a six-month extension or more, which could make it hard for the Senate to come to an agreement.

—This story was updated at 10:20 a.m.