Deep Research

Deep Research lets the AI agent conduct comprehensive, multi-source research on any topic — combining web sources, your vault notes, or both — and produce a structured markdown report with citations.

Note: Deep Research is not instant. A single research request typically takes several minutes as the API performs multiple rounds of searching, reading, and synthesizing information.

How It Works

1. You ask the agent to research a topic
2. The agent invokes the deep_research tool (with your confirmation)
3. Google's Deep Research API performs multiple search rounds, analyzing and synthesizing sources
4. A structured markdown report is generated with inline citations
5. Optionally, the report is saved to a file in your vault and added to the session context

This is fundamentally different from the regular Google Search tool, which returns quick single-query results. Deep Research performs iterative, multi-turn investigation — more like a research assistant spending time in a library than a quick web search.

Getting Started

Deep Research is always available as long as you have a valid API key configured. No additional setup is required for web-only research.

To include your vault notes in research, you'll need Semantic Vault Search enabled and your vault indexed.

Research Scopes

The tool supports three research scopes:

Scope	What it searches	When to use
both (default)	Web + vault notes	Best for most research — combines external knowledge with your existing notes
web_only	Web only	When your topic is outside your vault's scope
vault_only	Vault notes only	When you want to synthesize purely from your own notes (requires Semantic Search)

If you request both but Semantic Search isn't configured, the tool automatically falls back to web-only research.

Usage

Just ask the agent naturally. It will decide when to use Deep Research based on your request:

You: Research the latest developments in quantum error correction
     and save it to Research/quantum-error-correction.md

Agent: I'll conduct deep research on this topic. This may take a few minutes.
[Requests confirmation]
[Researches across multiple web sources]

Here's what I found: [structured report with citations]
The report has been saved to Research/quantum-error-correction.md

Example Prompts

Web + vault research (default):

Research how RAG architectures compare to fine-tuning for domain-specific tasks

Web only:

Do web-only deep research on the 2024 Nobel Prize in Physics

Vault synthesis:

Using only my vault notes, research and synthesize my findings on project management methodologies

With output file:

Research the history of the Zettelkasten method and save it to Reference/zettelkasten-history.md

Output Format

Research reports are structured as markdown:

# [Your Research Topic]

_Generated on [Date]_

---

[Synthesized findings organized into sections...]

Sources are cited inline with links to original URLs.

When you specify an output file:

• The report is saved to that path in your vault
• A .md extension is added automatically if missing
• The file is added to your current session context, so the agent can reference the findings in follow-up messages
• Protected folders (.obsidian, plugin state folder) cannot be used as output paths

How It Differs from Google Search

	Deep Research	Google Search
Depth	Multi-turn, iterative investigation	Single query
Time	Several minutes	Instant
Output	Structured report with citations	Search result snippets
Vault access	Can search vault via Semantic Search	No vault access
Best for	Comprehensive understanding of a topic	Quick factual lookups

The agent has both tools available and will choose the right one based on your request. A question like "what year was Python created?" gets a quick Google Search, while "research the evolution of Python's type system" triggers Deep Research.

Limitations

• Takes time — Expect several minutes per research request. The API performs multiple rounds of searching and analysis.
• Rate limits — Subject to Google API rate limits. If you hit a quota, you'll get a clear error message.
• Vault scope requires Semantic Search — The vault_only and vault portion of both scope require Semantic Vault Search to be enabled and your vault indexed.
• Citation accuracy — Citations come from Google's API. While generally reliable, always verify critical facts against original sources.
• No individual file deletion — Research reports saved to your vault are regular markdown files you can edit or delete freely.

Troubleshooting

"Deep research service not available"

The service failed to initialize. Check that your API key is valid in Google AI Studio.

"Research quota exceeded"

You've hit Google's API rate limit. Wait a few minutes and try again, or enable billing on your API key for higher quotas.

"vault_only scope requires RAG indexing"

You requested vault-only research but Semantic Vault Search isn't configured. Either:

• Enable and configure Semantic Vault Search, or
• Use web_only or both scope instead

Research takes very long or seems stuck

Deep Research is inherently slow — it's performing thorough multi-source investigation. If it takes more than 10 minutes, there may be an API issue. Check the developer console (Ctrl/Cmd + Shift + I) with Debug Mode enabled for details.

Report was generated but file wasn't saved

The research succeeded but saving failed. Check that:

• The output path isn't in a protected folder (.obsidian, plugin state folder)
• You have write permissions to the target directory
• The research results are still available in the chat — you can copy them manually