This paper focuses on the development of a Unified Inputs for WRF-Chem (UIWRF-Chem) system to support the MAIA satellite mission. The authors propose a framework that integrates NASA’s GEOS-FP and MERRA-2 as initial and boundary conditions, incorporates a stand-alone emissions preprocessor, updates land surface properties, and implements a new NOₓ emission scheme. They test the system’s performance across four MAIA target cities.

Overall, this is a solid and technically sound study. The authors demonstrate a good understanding of the different options available in WRF-Chem and the key differences among them. However, the manuscript currently suffers from a lack of clarity, particularly in the Introduction and Model Description sections. I recommend major revisions before it can be considered for publication.

General Comments:

1. Clarify the link to MAIA mission needs. Since the core purpose of this study is to support the MAIA mission, the paper should better articulate MAIA's specific modeling requirements—e.g., what variables are most relevant, what forecast capabilities are needed, and how UIWRF-Chem is designed to meet those needs.
2. Improve the Introduction. The rationale for modifying WRF-Chem is not clearly laid out. The authors should explain why it is necessary to update land surface properties, emissions modules, and boundary/initial conditions in the context of MAIA. A clearer articulation of these needs would better frame the scientific motivation.
3. Reorganize the Model Description section. The current presentation of model improvements is confusing. I suggest breaking it into clearly labeled subsections, each focused on a single enhancement (e.g., emissions, boundary conditions, NOₓ scheme, land surface update).
4. Quantify significance of improvements. While the paper compares results from different modeling schemes, it does not provide evidence of whether the differences are statistically significant or robust across other regions or time periods.

Specific Comments:

1. Why use WRF-Chem v3.8.1? Given that WRF-Chem versions above 4.0 are now available (with improvements such as subgrid-scale chemical transport for KF and GF schemes), the authors should justify why UIWRF-Chem is based on v3.8.1. Even though they mention plans to test GF in the future, a more detailed explanation is needed.
2. Summarize model setup in a table. Please consider adding a summary table listing the model configuration (e.g., resolution, land surface model, physics schemes, emissions setup, etc.), or update Table S2 accordingly.
3. Highlight novelty of new modules. Some of the newly added components appear to be simple integrations into WRF-Chem rather than innovations. The paper should more clearly highlight what is original and novel in this system.
4. Table S1. Please consider highlighting the best-performing configurations for easy comparison.
5. Figure 5: The comparison may be misleading due to resolution differences—MERRA-2 is coarse and likely underestimates high PM₂.₅ values, whereas WRF-Chem has higher resolution and better captures spatial variability. Consider interpolating WRF-Chem output to the MERRA-2 grid for a fair comparison, or include scatterplots at matched resolution.
6. Figure 6: Please emphasize the observational data (e.g., bold lines or larger markers) to improve readability.
7. Line 720: Consider discussing why the updated system better captures the observed PM₂.₅ peaks. This would strengthen the case for the model improvements.
8. Line 1035: It would be helpful to summarize the sensitivity tests in a table for easier interpretation.
9. MAIA compositional data: Since MAIA will retrieve PM component information, the paper should demonstrate how UIWRF-Chem simulates PM species. It would be useful to show comparisons against ground-based observations (e.g., from the IMPROVE network).
10. Significance testing: The paper discusses improved performance for certain configurations, but lacks significance tests to demonstrate that the improvements are statistically meaningful. This is important to ensure the optimal setup is not case-specific.

Zhang et al. present UI-WRF-Chem, a set of unified inputs (initial and boundary conditions) for WRF-Chem in support of the MAIA satellite mission. UI-WRF-Chem provides meteorological inputs as well as emissions; land surface data; and a new soil NOx emissions scheme. A new chemistry scheme based on MADE/SORGAM is also developed, MADE/SORGAM-DustSS, to incorporate GOCART-AFWA emission scheme for matching with the MERRA-2/GEOS-FP dust size bins.

The manuscript details many improvements to provide inputs to WRF-Chem. Of particular note is the development of WEPS as an emissions pre-processor which resolves a point of frustration in offline emissions processing for WRF-Chem. In addition, to support the MAIA satellite mission, UI-WRF-Chem extensively incorporates data from GEOS-FP and MERRA-2 products to the WRF-Chem model pipeline and evaluates many of these developments. These improvements have also been validated in four extensive case studies across the globe. The manuscript is well written and I recommend its publication.

Major comments:

1. The authors evaluate throughout the effect of incorporating "MERRA-2 chemical boundary conditions" into the simulation. Just to confirm that the simulations marked "none" mean zero boundary conditions are input; is this usual in WRF-Chem simulations? Does the common approach of using CAM-chem/WACCM outputs as boundary conditions provide no information for the dust and other aerosols in a WRF-Chem simulation? If CAM-chem/WACCM, as global models, can provide some kind of information, I think it would be a more fair comparison as to whether these conditions can/can not help the regional model capture the long-range transport event.

2. UI-WRF-Chem extensively integrates outputs from GEOS-FP and MERRA-2 as inputs for WRF-Chem; many of these improvements are not trivial, e.g., the updates to land input data, a new soil NOx emissions scheme, etc... Do the authors plan to contribute this capability to WPS and the WRF mainline model code in the future?

3. WEPS builds on the existing WRF-Chem emissions processing tools to incorporate several global inventories, as well as allowing NEI and MEIC inventories to replace the global inventory. Is the process of regional inventories to override the global inventory an automated process (i.e., a regional netCDF file can be supplied and it'll overwrite the global inventory?) like in GEOS-Chem's emissions tool, HEMCO, or code changes will be needed? How extensible is WEPS to update with further inventories, and how easy is it to update inventores in the future? For example, I noted that FINN v1.01 is supported but not the more recent FINN v2.5 - will WEPS enable an easier update of the inventores for ingestion into WRF-Chem?

4. I also suggest some presentation improvements: organize the best configuration (of model physics) for each case study domain in a table; also label in the figures the D1 and D2 domains for each case study; at times D1 is the whole region and D1 is marked by a rectangle and inset text could help the reader.

Specific/Minor comments:

L40: "because of" -> I suggest "enabled by".

L223-225: It's not clear what the paragraph is suggesting here. Are you suggesting that the manuscript's use of GEOS-FP and MERRA2 differs from the common practice of using CAM-chem/WACCM outputs as chemical IC/BC (which I believe is the common practice in the WRF-Chem user's guide) or that GEOS-FP and MERRA-2 are different in that they assimilate satellite-based aerosol fields? I would suggest revising this paragraph for clarity.

L425: "sea seal" -> "sea salt"?

L446: "relative humanity" -> "relative humidity"?

L519: "the chemistry will be transported..." -> maybe "the chemical tracers will be transported"?

SI Table S1 Los Angeles Simulation #1: "Li" -> "Lin"