Stop the agent or job from an external control, isolate the affected machine or runner, preserve evidence, and treat every credential the process could read as potentially exposed. Do not rely on the agent to stop itself, and do not assume that uninstalling the package cleans the system. Scope where the package was installed or executed, rotate accessible secrets from a trusted environment, restore a verified-safe dependency, investigate follow-on activity, and resume only after security review.
What should I do if my AI agent installed a malicious package?
Use this order. It is designed for a developer workstation, build runner, CI/CD pipeline, or service where an AI coding agent can install dependencies or run shell commands.
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- Stop agent actions and contain the environment. Disable the agent, workflow, runner, or job through a control outside the model. If the incident occurred in CI/CD, pause affected jobs and block deployments. Isolate the host, service, credential, or network segment according to the suspected exposure.
- Preserve evidence before cleanup. Record the package, version, package manager, install command, timestamps, lockfile changes, prompts, tool calls, terminal output, build logs, host or runner identity, and the credentials and data available to the process.
- Map the blast radius. Check direct and transitive dependencies, lockfiles, package caches, artifact repositories, developer machines, test and build systems, production systems, and every CI/CD job that could have consumed the package.
- Assume reachable secrets may be compromised. Revoke and reissue affected source-control, package-registry, cloud, SSH, API, environment, and CI/CD credentials from a trusted device or environment. Review audit logs for unauthorized use.
- Restore a known-safe state and investigate. Pin a verified-safe package version, remove malicious artifacts and affected caches where appropriate, then hunt for suspicious files, processes, network connections, workflow changes, and persistence.
- Escalate and obtain approval before resuming. Security or incident-response staff should review cause, scope, corrective actions, and any legal, regulatory, contractual, or customer-notification obligations.
The U.S. Department of Energy GEAR AI Security and Safety guidance summarizes the first decision well: “Stop or disable the workflow. Use the external kill path; do not rely on the model or agent to stop itself.”
1. Stop the agent and contain the affected environment
Use an external kill path
Terminate the agent session, revoke its job permission, disable the automation, or pause the pipeline from an administrative control. Do not ask the same agent to investigate or clean up first. A malicious install script or package can continue running, launch child processes, alter files, or use the agent’s own tools.
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Containment should match the exposure. Disconnect or quarantine a developer workstation if it had broad network or credential access. Disable a compromised runner or service account if the event was confined to CI/CD. Prevent deployment of artifacts produced during the suspect window. Preserve the state of the host or runner when practical instead of immediately rebuilding it; rebuilding can destroy useful evidence.
The Cyber Security Agency of Singapore’s 7 April 2026 advisory puts the operational rule plainly: “Isolate systems confirmed or suspected to be running trojanised packages until investigation and remediation are completed.” Follow your organization’s incident procedure if it specifies a different emergency control.
2. Preserve evidence and establish what actually ran
Capture the installation story
Before deleting files, collect:
- Package name, exact version, registry or repository, package manager, and install or update command.
- Direct and transitive dependency entries, lockfile diffs, manifests, integrity hashes, and package-manager logs.
- Time of installation, import, build, test, and deployment; the affected host, container, runner, branch, and job ID.
- AI-agent prompts, approvals, tool calls, shell history, terminal output, and files the agent created or changed.
- Build logs, endpoint telemetry, process trees, DNS and network records, cloud audit events, and source-control or workflow changes.
- Credentials, tokens, environment variables, files, repositories, and services that the process could read.
A package appearing in a lockfile does not prove that its code executed. Determine whether it was only resolved, downloaded, installed, imported, built, tested, or run in production. Logs and environment-specific investigation are needed; there is no universal inference method for every ecosystem.
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Search every place the dependency could exist
| Area | Checks to perform | Why it matters |
|---|---|---|
| Developer machines | Package-manager caches, working trees, virtual environments, local agent workspaces, shell history, and endpoint process and network logs | A workstation may expose source code, SSH keys, cloud credentials, and personal access tokens |
| CI/CD | All jobs using the lockfile or registry, ephemeral runners, injected secrets, build artifacts, caches, and deployment records | A short-lived runner can still leak every secret injected into that run |
| Test and build systems | Dependency mirrors, artifact repositories, test fixtures, generated files, and child processes | Build-time execution can modify artifacts or access signing and release credentials |
| Production | Images, deployed bundles, runtime logs, package directories, service accounts, and outbound connections | Runtime access may expose customer data or production infrastructure |
CISA has advised reviewing developer machines and pipelines that ran a compromised install. The Singapore advisory likewise recommends determining where a package was installed or executed. Include machines that received a cached or mirrored copy even if they did not fetch it directly from the public registry.
3. Which credentials should I rotate?
If malicious code ran where a secret was readable, treat that secret as exposed unless logs prove otherwise. Coordinate with incident response, then revoke and reissue from a trusted environment using the organization’s approved process. Rotation is not complete until old credentials are disabled and dependent systems use the replacements.
| Credential class | Examples to assess |
|---|---|
| Source control | Personal access tokens, deploy keys, repository and organization tokens, signing keys, and webhook secrets |
| Package ecosystem | Registry tokens, publish credentials, provenance or signing keys, and private-registry passwords |
| Cloud and infrastructure | Cloud-provider keys, infrastructure-as-code secrets, orchestration tokens, container-registry credentials, and database passwords |
| Developer access | SSH keys, local credential stores, VPN credentials, API keys, and environment-file secrets |
| CI/CD | Pipeline variables, runner registration tokens, deployment keys, service-account credentials, and secrets injected into the affected job |
Do not limit the review to the developer’s obvious credentials. CISA’s 2026 supply-chain advisory enumerates cloud-provider, registry, infrastructure, orchestration, source-control, and pipeline secrets. The correct set depends on what the affected process could access, including inherited environment variables, mounted files, metadata services, and agent-connected tools.
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For an ephemeral CI job, CISA’s Axios alert says to rotate all secrets injected into the compromised run. Review account, repository, workflow, cloud, and registry audit activity for use of either the old or new credentials. Look for new deploy keys, changed branch protections, altered workflows, unexpected package publications, unusual cloud roles, and access from unfamiliar locations.
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Replace the package safely
- Identify a package version verified as safe by the package maintainer, registry advisory, or your incident-response team.
- Update the manifest and lockfile, then pin the approved version using the project’s normal dependency controls.
- Remove malicious package directories, generated artifacts, and affected cache entries where appropriate.
- Rebuild from a trusted source and verify the resulting dependency tree and artifact integrity before deployment.
CISA’s package-specific Axios instructions include downgrading to known-safe versions and removing a known malicious dependency directory. Those exact versions and commands apply only to that incident; do not reuse them for a different package without checking its current advisory.
Deleting node_modules, running an uninstall command, or reinstalling dependencies is not proof that a host is clean. Malicious code may have copied secrets, changed workflow files, created persistence, launched another process, or sent data elsewhere before removal. If the host’s integrity cannot be established, preserve it for forensics and rebuild from a trusted image according to your response team’s direction.
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5. Investigate follow-on activity
Search endpoint, build, source-control, cloud, and network telemetry for activity during and after installation:
- Unexpected child processes, shell commands, interpreters, archive tools, credential-store access, or attempts to invoke local developer utilities.
- Outbound connections to unfamiliar domains or IP addresses, unusual DNS lookups, large uploads, and connections outside the normal build pattern.
- New or modified workflow files, scheduled tasks, startup scripts, hooks, package publication settings, branches, deploy keys, or access policies.
- Reads of source repositories, environment files, cloud metadata, SSH material, package-manager configuration, and CI/CD secret stores.
- Unusual package publication, account-login, repository, cloud, or deployment events.
CISA recommends forensic review of CI/CD logs, cloud audit trails, and developer machines in its 2026 supply-chain alert. Its Axios advisory also calls out unexpected child processes and anomalous network activity. Preserve timestamps and correlate them with the agent’s prompts and tool calls so investigators can distinguish intended build actions from malicious behavior.
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An AI coding agent can make a dependency incident broader when it has shell, filesystem, browser, or other tool permissions. The package runs under the permissions of the developer account, runner, container, or service that installs or imports it. The agent may also be abused indirectly if malware discovers local agent command-line tools, prompts, configuration, or connected repositories.
Snyk’s analysis of the 2025 Nx incident reported that malicious package code attempted to invoke local AI-agent command-line tools with unsafe flags to scan sensitive paths and exfiltrate data. That is a documented incident example, not evidence that every package or agent behaves this way. Your investigation should therefore ask both “What did the package do?” and “What could the agent, host, and connected tools do from that context?”
Escalation, notification, and the decision to resume
Notify your security operations or incident-response team as soon as containment is in place. If you lack internal capability, seek qualified incident-response help with verified software-supply-chain experience, developer-endpoint and CI/CD investigation capability, sound evidence-handling practices, appropriate geographic and contractual coverage, and availability that matches the incident. No single provider or product is automatically suitable.
Assess legal, regulatory, contractual, and customer-notification duties based on the data, systems, and jurisdictions involved. Keep the agent, affected workflow, and deployment path disabled until reviewers have documented:
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- Root cause and the package versions and environments involved.
- Whether code executed and what files, secrets, systems, and data it could access.
- Credential revocation and reissuance status, including audit findings.
- Host, artifact, repository, and pipeline remediation.
- Monitoring or control changes that reduce recurrence risk.
- Required approvals and any notifications.
Resume in a controlled manner: use clean workers or rebuilt hosts, approved dependencies, least-privilege credentials, and enhanced monitoring. A normal-looking build is not sufficient evidence of recovery.
Prevention after recovery
- Pin and review dependencies. Commit lockfiles, require review before adopting new third-party packages, and audit direct and transitive dependencies regularly.
- Reduce permissions. Give agents, developers, service accounts, and runners only the access required for the task. Separate development, test, and production roles and keep production secrets out of ordinary development jobs.
- Examine package provenance. Review maintainers, release history, ownership changes, install scripts, suspicious updates, and unnecessary production dependencies.
- Monitor execution and egress. Alert on unusual child processes, workflow changes, secret access, package publication, and outbound traffic from builds.
- Harden npm installations where appropriate. CISA’s April 2026 Axios alert recommended
ignore-scripts=trueandmin-release-age=7in.npmrc. These are npm-specific controls: ignoring lifecycle scripts can break packages that legitimately require them, and a seven-day release age does not stop every malicious package or execution path. - Maintain an agent kill path. Administrators should be able to revoke agent, runner, token, and deployment access without asking the model to cooperate.
What recent incidents show
- CISA’s 2025 Shai-Hulud alert said the worm had compromised more than 500 packages. That figure describes that incident, not the total number of malicious packages.
- The Cyber Security Agency of Singapore reported that a September 2025 compromise spread from an injected install script to more than 180 npm packages.
- Snyk’s account of the 2025 Nx incident described eight malicious Nx and Nx Powerpack releases that remained available for approximately 5 hours and 20 minutes before removal.
These cases illustrate why package removal alone is inadequate: compromise can involve install-time execution, credential theft, CI/CD propagation, agent tooling, and downstream artifacts.
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