The Senate Appropriations Committee plans to begin marking up spending bills Tuesday, starting off a grueling September that will include debate on more than $1.3 trillion in spending.

All that work will be capped off with a stopgap spending bill to avoid a partial government shutdown and give House and Senate lawmakers more time to work out the spending level and policy differences between the yet-to-be-released Senate bills and the legislation House appropriators marked up earlier this year.

When those conference negotiations get underway, appropriators will have to wade through a series of politically challenging issues that have widespread implications for national security, public health and immigration.

Among the key issues on the table:

The wall

Despite the bipartisan budget deal struck in July, border barrier spending — the issue that sparked the last shutdown — is still at the top of everyone’s watch list for major disputes this fall. Funding levels are very much in play as well as whether lawmakers will restrict the reprogramming authority President Donald Trump used earlier this year to divert money from various unrelated accounts to wall construction.

The Trump administration requested a total of $8.6 billion in wall funding for fiscal 2020; House Democrats’ counter includes $0. For the current fiscal year, by comparison, lawmakers and the White House settled on $1.375 billion.

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West Virginia Republican Shelley Moore Capito, who chairs the Senate Homeland Security Appropriations Subcommittee, expects the bill won’t advance until “the very end” of the process. “I think it’s going to be a problem,” she said before leaving for the August recess.

Negotiators were able to reach agreement in February on border barrier spending, but Trump declared a national emergency at the border and sought to transfer up to $6.7 billion in funding from other places, primarily Pentagon accounts. The Supreme Court has already upheld the administration’s ability to shift $2.5 billion from counterdrug operations, and on Sept. 3 the Pentagon announced it would delay spending some $3.6 billion previously set aside for military construction projects and instead use the money for wall construction.

However, House Democrats wouldn’t provide the $3.6 billion the White House wants to backfill those stalled projects, and are seeking to eliminate the administration’s ability to reprogram any funding for border barrier construction altogether. They’ve also proposed reducing the Pentagon’s transfer authority from $9.5 billion to $1.5 billion.

Abortion access

Democrats have added a host of policy provisions to their spending bills that seek to protect funding for organizations — both domestically and abroad — that include abortion as a family planning option.

Among the possible fights is a provision in the Labor-HHS-Education bill that would require the Trump administration to distribute Title X family planning grants without considering whether a health care organization offers abortions. The administration had previously finalized regulations to bar federal funds for clinics that perform abortions or refer patients to other providers for abortion services.

The House bill would ensure that groups like Planned Parenthood — the largest Title X provider, which has already opted out of the program as a result of the new HHS rule — can continue receiving grants. Democrats are also hoping to prevent a rule from taking effect that would protect health care workers who opt out of participating in services that are against their religious beliefs, such as abortion.

On the international side, Democrats want to overturn the Trump administration’s revised “Mexico City policy” rule, which bars a host of foreign assistance funding for overseas nongovernmental organizations that promote or provide abortion services. That provision, in the House-passed State-Foreign Operations measure, will also likely prove a bone of contention in talks with the Senate and White House.

Immigration policy

A limit on Immigration and Customs Enforcement’s detention capacity was one of the hardest issues to resolve during the fiscal 2019 process, with lawmakers finally reaching agreement to ratchet down the average daily population in ICE facilities to 40,520 by the end of the fiscal year. But ICE has in fact been moving in the opposite direction, including transferring extra funds to help support a detainee population that surged to almost 55,000 at one point in August. That move will likely make negotiations over fiscal 2020 funding all the more complicated; the administration requested a 54,000-bed average daily capacity for fiscal 2020, while House Democrats included funding for ICE to detain only about 34,000 people on average in their bill.

House Democrats are also attempting to stop the Homeland Security Department from implementing the so-called public charge rule, which would allow immigration authorities to block entry to the United States or deny green cards for legal permanent residency to anyone who might someday use noncash public benefits, such as Medicaid, food stamps or low-income housing.

The administration is also moving forward with a controversial rule to redefine standards of care for migrant children in custody, seeming to overturn the 1997 court settlement known as the Flores agreement, which limits the amount of time children can remain in custody to 20 days. Critics are calling on lawmakers to block the move in the fall spending battle.

Gun regulations

Several mass shootings marred the August recess, with calls for legislative action growing louder once again. It’s unclear whether the Senate will be able to move stand-alone legislation, though it’s possible legislation to toughen background checks, among other measures, could spill over into the appropriations process.

Either way, gun violence research and prevention funding will likely be a point of contention in the Labor-HHS-Education spending bill. House Democrats backed a $50 million line item — the first such appropriation in more than two decades. House Labor-HHS-Education Appropriations Chairwoman Rosa DeLauro, a Connecticut Democrat, has vowed to fight for the money despite a lower overall allocation for nondefense funds as part of the budget deal.

Senate Labor-HHS-Education Appropriations Chairman Roy Blunt, a Missouri Republican, believes HHS can research gun violence without congressional direction, but said he hopes controversial issues don’t delay his subcommittee’s bill, which became law on time last year for the first time since 1996.

“The reason our committee was so successful last year is that we made the decision early to not open the bill to controversial issues. I’m hopeful we do the same thing this year, which would mean we wouldn’t change things that have been traditionally in the bill or attempt to fund partisan priorities,” Blunt said.

Andrew Siddons contributed to this report.