• The precedent from the wider PMIP and CMIP efforts does not include phase numbering. Bear in mind that all phase 2 data is stored within a specific directory (L391).
• No period is included in the name. This is especially pertinent, as I understood the Miocene is also included in DeepMIP. Since you focus only on the EECO, why not choose either 'eocene' or 'EECO' instead of deepmip  
• I find the inclusion of 'stand' to be unhelpful. I can understand defining subsidiary experiments, with a 'sens' flag. Surely this implicitly assumes that other than the named feature being changed, everything else is as set as standard - inconsistent with the requirement of a 'stand' flag.
• If you do choose to allow ESGF inclusion, your main experiment name will be the longest around (and will not make sense to people not involved in deepMIP).    

General Comments

This manuscript presents the experimental design for Phase 2 of the DeepMIP–Eocene initiative, outlining updated boundary conditions, simulation protocols, and scientific motivations for investigating early Eocene climate. Overall, the paper is clearly written, well‑structured, and highly valuable to the paleoclimate modelling community. Justification for focusing solely on the EECO is strong, the boundary condition updates are explained in a logical and transparent manner, and the connection to Phase 1 findings is thoughtfully presented. The manuscript also provides a clear link between deep‑time model intercomparison and broader climate questions such as equilibrium climate sensitivity and the evaluation of model behaviour under high‑CO₂ states.

While the paper is comprehensive, there are areas where clarity could be improved or where additional elaboration might benefit readers, as described below. 

Specific Comments

Introduction

L20: The Mallory reference is perhaps belittling the importance of learning about processes and mechanisms that led to things being the way they were/are even if they are not so directly relevant for future climate change. I suggest removing.

L76-78: Do we have any idea why there are such differences in CO2 estimate for the best agreement with the data?

L97-98: Can you perhaps infer that this may be the cause of some disagreement between models?

L98: Over what period were the simulations run but still did not reach equilibrium?

L63-92: I wonder if this section could be reorganised into consistencies between models and data, consistencies between models but disagreement with data, inconsistencies between models (some of which may agree with the data), and inconsistencies between models and data so that is clearer what the main certainties and uncertainties are?

Figure 1: I presume the divergence in the colour scheme around the EOT is to highlight the shift from the greenhouse world to the icehouse world - might be worth adding those labels to the figure to explain why that was chosen as the divergence point.

Experimental Design

L122: Include Eocene/EECO in the simulation naming to avoid confusion with the other DeepMIP simulations. I believe MioMIP is using Deepmip-Mio, perhaps here therefore they should be Deepmip-Eo or Deepmip-EECO?

L254-244: Ambiguous as to whether you are suggesting that this runoff routing field could be used for Phase 2 or not

L270: What criteria is used to determine if regions have "sufficient" data coverage? A comment on the vegetation data availability for this period would also be useful

L330-331: Is the best-fit GCM CESM1.2 for Thomspon in BIOME4 the same as the best-fit GCM CESM1.2 for Brugger in LPJ-GUESS? If so, worth commenting on that.

L336-338: Are the discrepancies between the BIOME4 version of the vegetation and the data because these are where the model has been corrected towards the data in the LPJ-GUESS version of the vegetation? i.e. because the BIOME4 version has not undergone the hybrid proxy reconstruction correction step? Or are these different regions?

L362-363: You suggest that groups can use initial conditions from the Phase 1 model database, but in L98 you state that many models did not reach full equilibrium but the end of their simulations. Are there some models in the Phase 1 data that you would therefore recommend are NOT used for the initial conditions for Phase 2? Similarly, are there any in the database that suffered from crashing early or running away that should NOT be used? Or are these not in the database?

Figure 4: It is very difficult to see the details of the legends for (a) and (b), and the distinction between some of the greens is so small it is nearly impossible to discern which is which on the map. It also appears that the same colour has been used for Ice in (a) as Savannah in (b) and (c). Can you try to use a more distinctive colour scheme?

Figure 5: Similar comments on the colour scheme to Figure 4.

Summary and Plans for analysis

L416: This section is very short and the title is misleading. Perhaps Section 2.5 might fit better here. Maybe Summary and Next Steps or similar might be a better descriptor? 

L424: Are there plans to version control the proxy database so it is clear which dataset is being used for model-data comparisons and to ensure consistency between the analyses by different groups?

Figure A1. The colour scheme used may prove difficult for some colour blindness conditions.

Technical Corrections

Abstract 

L1-2: No commas required

L2: Define when the early Eocene is

L8: Word missing, a new vegetation... scheme/distribution/boundary condition

L10-12: Pluralisation of concentrations seems a little odd in the context of the model simulations where preindustrial CO2 is a constant and 4 x preindustrial CO2 is therefore also a constant.

Introduction

L38: Word missing, we/DeepMIP extend...

L38: Comma after Quaternary not required

L46: Word missing, also indicate

L47: No comma required before 'and a vegetation consistent' 

L47: Duplication of wording, perhaps change 'a generally warmer and wetter climate than modern' to something like 'those warmer and wetter conditions'?

L53: Is Herold the only reference for all these differences? Or do you mean to say Herold and references therein?

L55: No comma required before 'and has been used'

L61: No comma required before 'and have been discussed'

L70: Pluralisation of concentrations again

L73: Unnecessary 'and' before 'drier conditions'

Experimental Design

L120: Maybe introduce PI=preindustrial when talking about CO2 concentrations earlier in the manuscript

L157 & 161: Inconsistent wording, runaway versus 'runs away'. Maybe also explain what this term means.

L173: Typo, Appemdix

L200: Wrong wording?, should be 'or between' rather than 'as well as between'

L205-206: Incorrect wording, 'As the paleogeographic reconstructions used here all have modified' should be 'As all the paleogeographic reconstructions used here have modified'

L222: Commas needed around the word 'particularly'

L227: No comma needed after the word 'resolved'

L286-289: The long sentence is a little confusing. Perhaps reword to something like 'The recommendations for all other boundary conditions remains unchanged from Phase 1 (refer to Lunt et al. 2017). Using the section numbering from Lunt et al. (2017), detailed recommendations are given for soils and lakes in Section 4.2.2,' etc